This run was generated using rMAP version performed on 2021-09-04… Thank you for using this pipeline!!


Assembly summary statistics


Field Description
SampleID Name of the sample
TrimReads Total number of reads after quality filtering
MeanReadLen Average read length after quality filtering
Contigs Number of contigs of the draft genome (>200bp)
GenomeLength Length (bp) of the draft genome
LargestContig Length (bp) of the largest contig in the genome
N50 Length of the smallest contig in the set that contains the fewest (largest) contigs whose combined length represents at least 50% of the assembly
GC-Content GC content (%) of the draft genome
Depth Number of times each nucleotide position in the draft genome has a read that aligns to that position


SampleID TrimReads MeanReadLen Contigs GenomeLength LargestContig N50 GC-Content Depth
ID003II 440193 235 2738 11624023 93753 10830 55.68 8X
ID012II 189432 229 74 4027781 364375 119014 39.01 10X
ID014II 372138 222 538 9335120 199730 41879 44.26 8X
ID030 658388 226 1953 7910850 164063 11044 53.55 18X
ID063 404133 239 146 4729069 314511 101315 50.83 20X
ID089 342534 223 135 4796271 223487 90807 37.92 15X
ID186 336786 232 45 3883370 473175 202592 38.93 20X
ID259 461494 239 289 5033855 131448 38437 55.64 21X
ORTHO015E 206893 219 81 3977132 340368 123633 39.09 11X
ORTHO037E 407540 218 54 3886703 358132 155954 38.94 22X
ORTHO047E 443635 240 364 5147002 147377 32206 55.08 20X
ORTHO05E 1031 249 377 137839 2786 362 40.19 1X
ORTHO082EII 150557 244 3692 9881394 65119 5466 61.88 3X

Select the parameter

Number of reads

Average number of reads per sample = 339596

Average read length

Average read length per sample = 232 bp

Number of contigs

Average number of contigs per sample = 807

Genome length

Average genome length per sample = 5720801 bp

Largest contig length

Average largest contig length per sample = 221410 bp

N50

Average N50 per sample = 71811 bp

GC content

Average GC content per sample = 47%

Sequencing depth

Average sequencing depth = 13.615X

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SNP-variant calling


Field Description
GenomePosition Position in the genome where SNP is found
Type Nature of the SNP identified (Only ‘True’ SNPs are shown by default)
ReferenceAllele Allele found in the reference genome
AlternateAllele Allele found in the genome of interest forming the SNP
Consequence Amino acid alterations caused by the SNP
AffectedGene The tartget gene affected by the SNP
Product The outcome from the presence of the SNP


Select the sample

ID003II
## Error in read.table("ID003II_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(snps): object 'snps' not found
## Error in cbind(snps[, 1:7]): object 'snps' not found
## Error in colnames(snpsdata) = c("GenomePosition", "Type", "ReferenceAllele", : object 'snpsdata' not found
## Error in eval(expr, envir, enclos): object 'snpsdata' not found
## Error in row.names(snps) = NULL: object 'snps' not found
## Error in nrow(snps): object 'snps' not found
ID012II
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID014II
## Error in read.table("ID014II_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID030
## Error in read.table("ID030_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID063
## Error in read.table("ID063_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID089
## Error in read.table("ID089_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID186
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ID259
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GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ORTHO015E
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe NA copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile NA copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn NA copper resistance protein NlpE N-terminal domain-containing protein
61728 snp T C missense_variant c.4274066A>G p.His1424689Arg NA copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn NA copper resistance protein NlpE N-terminal domain-containing protein
61930 snp G A missense_variant c.4273864C>T p.Pro1424622Ser NA copper resistance protein NlpE N-terminal domain-containing protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu NA quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val NA quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser NA quaternary ammonium compound resistance protein
2147520 snp G T missense_variant c.2188274C>A p.Ala729425Glu NA quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu NA quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu NA quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp NA quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln NA quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro NA quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe NA quaternary ammonium compound resistance protein
2147613 snp A G missense_variant c.2188181T>C p.Val729394Ala NA quaternary ammonium compound resistance protein
3296382 snp C T missense_variant c.1039412G>A p.Arg346471Gln NA HdeD family acid-resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His NA HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser NA HdeD family acid-resistance protein
3296631 snp T A missense_variant c.1039163A>T p.His346388Leu NA HdeD family acid-resistance protein
3296659 snp C T missense_variant c.1039135G>A p.Val346379Ile NA HdeD family acid-resistance protein
3296712 snp C T missense_variant c.1039082G>A p.Arg346361Gln NA HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu NA HdeD family acid-resistance protein
3296799 snp A C missense_variant c.1038995T>G p.Phe346332Cys NA HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val NA HdeD family acid-resistance protein
3296833 snp C T missense_variant c.1038961G>A p.Ala346321Thr NA HdeD family acid-resistance protein
3468201 snp A G missense_variant c.867593T>C p.Leu289198Pro NA organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala NA organic hydroperoxide resistance protein
3468244 snp A G missense_variant c.867550T>C p.Tyr289184His NA organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu NA organic hydroperoxide resistance protein
3504715 snp C T missense_variant c.831079G>A p.Val277027Ile NA copper resistance system multicopper oxidase
3504820 snp C T missense_variant c.830974G>A p.Gly276992Ser NA copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala NA copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val NA copper resistance system multicopper oxidase
3505542 snp T C missense_variant c.830252A>G p.Lys276751Arg NA copper resistance system multicopper oxidase
3505575 snp G A missense_variant c.830219C>T p.Thr276740Ile NA copper resistance system multicopper oxidase
3505587 snp A G missense_variant c.830207T>C p.Val276736Ala NA copper resistance system multicopper oxidase
3505642 snp G A missense_variant c.830152C>T p.Pro276718Ser NA copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met NA copper resistance system multicopper oxidase
3505861 snp C T missense_variant c.829933G>A p.Ala276645Thr NA copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala NA copper resistance system multicopper oxidase
3506433 snp T A missense_variant c.829361A>T p.Asp276454Val NA copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser NA copper resistance protein B
3506631 snp C T missense_variant c.829163G>A p.Gly276388Glu NA copper resistance protein B
3506650 snp G A missense_variant c.829144C>T p.Leu276382Phe NA copper resistance protein B
3506670 snp G A missense_variant c.829124C>T p.Pro276375Leu NA copper resistance protein B
3506688 snp T A missense_variant c.829106A>T p.Gln276369Leu NA copper resistance protein B
3506718 snp T C missense_variant c.829076A>G p.His276359Arg NA copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu NA copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met NA copper resistance protein B
3506809 snp G A missense_variant c.828985C>T p.Pro276329Ser NA copper resistance protein B
3506845 snp C G missense_variant c.828949G>C p.Ala276317Pro NA copper resistance protein B
3506886 snp G A missense_variant c.828908C>T p.Ala276303Val NA copper resistance protein B
3506895 snp C T missense_variant c.828899G>A p.Arg276300Lys NA copper resistance protein B
3506950 snp T C missense_variant c.828844A>G p.Ser276282Gly NA copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg NA copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr NA copper resistance protein B
3507176 snp G A missense_variant c.674G>A p.Gly225Glu NA copper resistance protein B
3507182 snp G A missense_variant c.680G>A p.Gly227Asp NA copper resistance protein B
ORTHO037E
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ORTHO047E
## Error in read.table("ORTHO047E_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ORTHO05E
## Error in read.table("ORTHO05E_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B
ORTHO082EII
## Error in read.table("ORTHO082EII_amr_snps", header = T, sep = "\t", dec = ".", : no lines available in input
GenomePosition Type ReferenceAllele AlternateAllele Consequence AffectedGene Product
61633 snp T A missense_variant c.4274161A>T p.Ile1424721Phe copper resistance protein NlpE N-terminal domain-containing protein
61642 snp A T missense_variant c.4274152T>A p.Phe1424718Ile copper resistance protein NlpE N-terminal domain-containing protein
61695 snp C T missense_variant c.4274099G>A p.Ser1424700Asn copper resistance protein NlpE N-terminal domain-containing protein
61761 snp A G missense_variant c.4274033T>C p.Ile1424678Thr copper resistance protein NlpE N-terminal domain-containing protein
61898 snp G A missense_variant c.374G>A p.Ser125Asn copper resistance protein NlpE N-terminal domain-containing protein
2147379 snp T C missense_variant c.2188415A>G p.Lys729472Arg quaternary ammonium compound resistance protein
2147454 snp G A missense_variant c.2188340C>T p.Pro729447Leu quaternary ammonium compound resistance protein
2147484 snp G A missense_variant c.2188310C>T p.Ala729437Val quaternary ammonium compound resistance protein
2147496 snp A G missense_variant c.2188298T>C p.Phe729433Ser quaternary ammonium compound resistance protein
2147520 snp G C missense_variant c.2188274C>G p.Ala729425Gly quaternary ammonium compound resistance protein
2147529 snp T A missense_variant c.2188265A>T p.Gln729422Leu quaternary ammonium compound resistance protein
2147538 snp G A missense_variant c.2188256C>T p.Ser729419Leu quaternary ammonium compound resistance protein
2147544 snp G T missense_variant c.2188250C>A p.Ala729417Asp quaternary ammonium compound resistance protein
2147559 snp A T missense_variant c.2188235T>A p.Leu729412Gln quaternary ammonium compound resistance protein
2147568 snp T G missense_variant c.2188226A>C p.His729409Pro quaternary ammonium compound resistance protein
2147574 snp G A missense_variant c.2188220C>T p.Ser729407Phe quaternary ammonium compound resistance protein
3296460 snp C T missense_variant c.1039334G>A p.Arg346445His HdeD family acid-resistance protein
3296469 snp G A missense_variant c.1039325C>T p.Ala346442Val HdeD family acid-resistance protein
3296550 snp A G missense_variant c.1039244T>C p.Leu346415Pro HdeD family acid-resistance protein
3296619 snp A G missense_variant c.1039175T>C p.Leu346392Ser HdeD family acid-resistance protein
3296656 snp T C missense_variant c.1039138A>G p.Lys346380Glu HdeD family acid-resistance protein
3296736 snp G T missense_variant c.1039058C>A p.Thr346353Lys HdeD family acid-resistance protein
3296763 snp G A missense_variant c.1039031C>T p.Pro346344Leu HdeD family acid-resistance protein
3296814 snp G A missense_variant c.1038980C>T p.Ala346327Val HdeD family acid-resistance protein
3442765 snp T G missense_variant c.893029A>C p.Ile297677Leu nreB nickel resistance MFS transporter NreB
3468029 snp C T missense_variant c.867765G>A p.Met289255Ile organic hydroperoxide resistance protein
3468216 snp A G missense_variant c.867578T>C p.Val289193Ala organic hydroperoxide resistance protein
3468231 snp T C missense_variant c.867563A>G p.Tyr289188Cys organic hydroperoxide resistance protein
3468300 snp G A missense_variant c.867494C>T p.Pro289165Leu organic hydroperoxide resistance protein
3504660 snp C A missense_variant c.831134G>T p.Cys277045Phe copper resistance system multicopper oxidase
3504723 snp C T missense_variant c.831071G>A p.Ser277024Asn copper resistance system multicopper oxidase
3505158 snp A G missense_variant c.830636T>C p.Val276879Ala copper resistance system multicopper oxidase
3505287 snp G A missense_variant c.830507C>T p.Ala276836Val copper resistance system multicopper oxidase
3505723 snp G C missense_variant c.830071C>G p.Leu276691Val copper resistance system multicopper oxidase
3505778 snp A G missense_variant c.1224A>G p.Ile408Met copper resistance system multicopper oxidase
3505887 snp T G missense_variant c.829907A>C p.Glu276636Ala copper resistance system multicopper oxidase
3505935 snp C T missense_variant c.829859G>A p.Gly276620Asp copper resistance system multicopper oxidase
3506327 snp C G missense_variant c.829467G>C p.Lys276489Asn copper resistance system multicopper oxidase
3506624 snp C G missense_variant c.829170G>C p.Arg276390Ser copper resistance protein B
3506688 snp T G missense_variant c.829106A>C p.Gln276369Pro copper resistance protein B
3506736 snp G A missense_variant c.829058C>T p.Pro276353Leu copper resistance protein B
3506761 snp G T missense_variant c.829033C>A p.Leu276345Met copper resistance protein B
3506781 snp A G missense_variant c.829013T>C p.Leu276338Pro copper resistance protein B
3506932 snp C A missense_variant c.828862G>T p.Asp276288Tyr copper resistance protein B
3506963 snp A G missense_variant c.461A>G p.Lys154Arg copper resistance protein B
3506979 snp T A missense_variant c.828815A>T p.Glu276272Val copper resistance protein B
3506995 snp C A missense_variant c.828799G>T p.Asp276267Tyr copper resistance protein B
3507025 snp C A missense_variant c.828769G>T p.Val276257Leu copper resistance protein B
3507039 snp C G missense_variant c.828755G>C p.Ser276252Thr copper resistance protein B


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Phylogenetic inference

Phylogenetic inference based on vcf SNPS

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Antimicrobial Resistance Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product
Resistance Antibiotic that the gene confers resistance to


Select the samples and the database

ID003II
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01177 71 931 aac(3)-IId_1 0/0 100.0 99.9 EU022314 aac(3)-IId Gentamicin, Tobramycin
contig00154 13860 14662 aadA2_1 0/0 98.0 99.9 NC_010870 aadA2 Streptomycin
contig00463 4721 5254 ant(2’’)-Ia_13 0/0 100.0 99.1 DQ176450 ant(2’’)-Ia Gentamicin, Tobramycin
contig00988 2040 2573 ant(2’’)-Ia_13 0/0 100.0 99.8 DQ176450 ant(2’’)-Ia Gentamicin, Tobramycin
contig00474 3794 4597 aph(3’’)-Ib_5 0/0 100.0 100.0 AF321551 aph(3’’)-Ib Streptomycin
contig01476 48 863 aph(3’)-Ia_7 0/0 100.0 100.0 X62115 aph(3’)-Ia
contig02215 25 783 aph(3’)-VIa_1 0/0 97.3 100.0 X07753 aph(3’)-VIa Amikacin
contig00474 2958 3794 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00988 1056 1922 blaCARB-2_1 0/0 100.0 100.0 M69058 blaCARB-2 Ampicillin, Amoxicillin, Piperacillin
contig00966 1160 1972 blaNDM-1_1 0/0 100.0 100.0 FN396876 blaNDM-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00812 1447 2277 blaOXA-1_1 0/0 100.0 100.0 HQ170510 blaOXA-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig01290 1049 1838 blaOXA-22_1 0/0 95.8 99.9 AF064820 blaOXA-22 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00197 9252 10094 blaOXA-420_1 0/0 100.0 100.0 AB983359 blaOXA-420
contig01773 33 848 blaOXA-60_1 0/0 100.0 100.0 AF525303 blaOXA-60 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem
contig00812 696 1328 catB3_2 0/0 100.0 99.8 U13880 catB3 Chloramphenicol
contig00192 1187 2452 cmlB1_1 0/0 100.0 99.8 AM296481 cmlB1 Chloramphenicol
contig01358 1213 1686 dfrA5_1 0/0 100.0 100.0 X12868 dfrA5 Trimethoprim
contig00785 1240 2453 floR_2 0/0 99.9 98.3 AF118107 floR Chloramphenicol, Florfenicol
contig01609 131 1052 mph(A)_2 1/1 100.0 99.6 U36578 mph(A) Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00891 111 995 mph(E)_1 0/0 100.0 100.0 DQ839391 mph(E) Erythromycin
contig00891 1051 2526 msr(E)_1 0/0 100.0 100.0 FR751518 msr(E)
contig01714 93 959 sul1_5 0/0 100.0 99.9 EU780013 sul1 Sulfamethoxazole
contig01812 316 1128 sul2_2 0/0 99.6 100.0 AY034138 sul2 Sulfamethoxazole
contig00971 143 1375 tet(31)_1 0/0 100.0 100.0 GQ283908 tet(31) Doxycycline, Tetracycline
contig00474 867 2042 tet(G)_2 0/0 100.0 100.0 AF133140 tet(G) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01177 71 931 AAC(3)-IId 0/0 100.0 99.9 EU022314.1:0-861 AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig00154 13860 14639 aadA2 0/0 100.0 100.0 AF156486:5012-5792 aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. aminoglycoside
contig00463 4721 5254 ANT(2’’)-Ia 0/0 100.0 98.9 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00988 2040 2573 ANT(2’’)-Ia 0/0 100.0 99.2 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00474 3794 4597 APH(3’’)-Ib 0/0 100.0 99.8 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig01476 48 863 APH(3’)-Ia 0/0 100.0 100.0 BX664015.1:103833-103017 APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp. aminoglycoside
contig02215 25 783 APH(3’)-VIa 0/0 97.3 100.0 X07753:102-882 APH(3’)-VIa is a plasmid-encoded aminoglycoside phosphotransferase in A. baumannii aminoglycoside
contig00474 2958 3794 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00988 1056 1970 CARB-3 0/0 100.0 99.9 S46063:121-1036 CARB-3 is a beta-lactamase found in Pseudomonas aeruginosa penam
contig00812 696 1328 catB3 0/0 100.0 99.8 JX101693.1:58200-58833 catB3 is a plasmid or chromosome-encoded variant of the cat gene found in Salmonella typhimurium Acinetobacter baumannii and Escherichia coli phenicol
contig00192 1187 2452 cmlB1 0/0 100.0 99.8 AM296481:775-2041 cmlB1 is a plasmid-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica phenicol
contig00966 1976 2341 determinant_of_bleomycin_resistance 0/0 100.0 100.0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide
contig01358 1213 1686 dfrA5 0/0 100.0 100.0 DQ278190:0-474 dfrA5 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine
contig00785 1239 2453 floR 0/0 100.0 99.9 AF231986:3307-4522 floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae phenicol
contig01609 147 1052 mphA 0/0 100.0 99.9 D16251.1:2531-1625 The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner. macrolide
contig00891 111 995 mphE 0/0 100.0 100.0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 macrolide
contig00891 1051 2526 msrE 0/0 100.0 100.0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00966 1160 1972 NDM-1 0/0 100.0 100.0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. carbapenem, cephalosporin, cephamycin, penam
contig00812 1447 2277 OXA-1 0/0 100.0 100.0 JN420336.1:2230-1399 OXA-1 is a beta-lactamase found in E. coli cephalosporin, penam
contig01290 1049 1838 OXA-22 0/0 95.8 99.9 AF064820:951-1776 OXA-22 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig00197 9252 10094 OXA-420 0/0 100.0 100.0 AB983359:2425-3268 From the Lahey list of beta-lactamases. Not yet released. cephalosporin, penam
contig01773 33 848 OXA-60 0/0 100.0 100.0 AF525303:2770-3586 OXA-60 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig01358 691 1023 qacH 0/0 100.0 99.4 DQ149925.1:188-521 qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae fluoroquinolone
contig01714 93 932 sul1 0/0 100.0 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig01812 316 1128 sul2 0/0 99.6 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00971 143 1375 tet(31) 0/0 100.0 99.8 AJ250203:1650-2883 Tet31 is a tetracycline efflux pump found in Aeromonas salmonicida a Gram-negative bacteria. It has also been shown to be expressed in Gallibacterium anatis. tetracycline
contig00474 867 2042 tet(G) 0/0 100.0 92.8 AF133139:0-1176 TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR sul1 and cmlA9 genes which encode proteins that can confer florfenicol/chloramphenicol sulfamethoxazole and chloramphenicol resistance respectively. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01177 71 931 (AGly)aac3-IId 0/0 100.0 99.9 EU022314:1-861 (AGly)aac3-IId NA
contig00812 2377 3181 (AGly)aadA1-pm 0/0 96.9 99.8 JQ690540:7968-8798 (AGly)aadA1-pm NA
contig00154 13860 14639 (AGly)aadA2 0/0 100.0 100.0 X68227:66-945 (AGly)aadA2 NA
contig00463 4721 5254 (AGly)aadB 0/0 100.0 98.9 JQ690540:4275-4808 (AGly)aadB NA
contig00988 2040 2573 (AGly)aadB 0/0 100.0 99.2 JQ690540:4275-4808 (AGly)aadB NA
contig01476 48 863 (AGly)aph(3’’)-Ia 0/0 100.0 100.0 FJ172370:38668-39483 (AGly)aph(3’’)-Ia NA
contig02215 25 783 (AGly)aphA6 0/0 97.3 99.9 JF949760:695-1474 (AGly)aphA6 NA
contig00474 3794 4597 (AGly)strA 0/0 100.0 99.9 AB366441:22458-23261 (AGly)strA NA
contig00474 2958 3794 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00966 1160 1972 (Bla)blaNDM-1 0/0 100.0 100.0 JQ080305:1-813 (Bla)blaNDM-1 NA
contig00812 1447 2277 (Bla)blaOXA-1 0/0 100.0 100.0 JQ682867:1-831 (Bla)blaOXA-1 NA
contig01290 1049 1838 (Bla)blaOXA-22 0/0 95.8 99.9 AF064820:952-1776 (Bla)blaOXA-22 NA
contig00197 9252 10094 (Bla)blaOXA-58 0/0 100.0 99.6 AY665723:3301-4143 (Bla)blaOXA-58 NA
contig01773 33 848 (Bla)blaOXA-60 0/0 100.0 93.1 AY664505:1-816 (Bla)blaOXA-60 NA
contig00988 1056 1970 (Bla)CARB-3 0/0 100.0 99.9 S46063:122-1036 (Bla)CARB-3 NA
contig01609 147 1052 (MLS)mph(A) 0/0 100.0 99.9 DQ445270:1626-2531 (MLS)mph(A) NA
contig00891 111 995 (MLS)mph(E) 0/0 100.0 99.9 JF769133:8777-9661 (MLS)mph(E) NA
contig00891 1051 2526 (MLS)msr(E) 0/0 100.0 100.0 JF769133:7246-8721 (MLS)msr(E) NA
contig00812 696 1328 (Phe)catB3 0/0 100.0 99.7 AJ009818:883-1515 (Phe)catB3 NA
contig00192 1187 2452 (Phe)cmlB1 0/0 100.0 99.8 NG_036292:776-2041 (Phe)cmlB1 NA
contig00785 1239 2453 (Phe)floR 0/0 100.0 99.8 AKLJ01000508:383-1597 (Phe)floR NA
contig01714 93 932 (Sul)sul1 0/0 100.0 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig01812 316 1128 (Sul)sul2 0/0 99.6 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00971 143 1375 (Tet)tet(31) 0/0 100.0 99.8 AJ250203:1651-2883 (Tet)tet(31) NA
contig00474 867 2042 (Tet)tetG 0/0 100.0 100.0 AF133140:757-1932 (Tet)tetG NA
contig00474 2146 2754 (Tet)tetR(G) 0/0 96.2 98.5 S52438:113-745 (Tet)tetR(G) NA
contig01358 1213 1686 (Tmt)dfrA5 0/0 100.0 100.0 X12868:1306-1779 (Tmt)dfrA5 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01177 71 931 aac(3)-IId 0/0 100.0 100.0 NG_047251.1 aminoglycoside N-acetyltransferase AAC(3)-IId GENTAMICIN
contig01358 48 602 aac(6’)-Ib-G 0/0 100.0 99.8 NG_051697.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase GENTAMICIN
contig00812 2390 3181 aadA1 0/0 100.0 99.9 NG_052266.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig00154 13860 14651 aadA2 0/0 100.0 100.0 NG_051846.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2 STREPTOMYCIN
contig00463 4721 5254 ant(2’’)-Ia 0/0 100.0 99.1 NG_052432.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00988 2040 2573 ant(2’’)-Ia 0/0 100.0 99.8 NG_047389.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00474 3794 4621 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig01476 48 863 aph(3’)-Ia 0/0 100.0 100.0 NG_047431.1 aminoglycoside O-phosphotransferase APH(3’)-Ia KANAMYCIN
contig02215 25 783 aph(3’)-VIa 0/0 97.3 100.0 NG_047448.1 aminoglycoside O-phosphotransferase APH(3’)-VIa AMIKACIN, KANAMYCIN
contig00474 2958 3794 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00988 1056 1922 blaCARB-2 0/0 100.0 100.0 NG_048722.1 PSE family carbenicillin-hydrolyzing class A beta-lactamase CARB-2 BETA-LACTAM
contig00966 1160 1972 blaNDM-1 0/0 100.0 100.0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1 CARBAPENEM
contig00812 1447 2277 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig01290 1049 1838 blaOXA-22 0/0 95.8 99.9 NG_049518.1 benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 BETA-LACTAM
contig00197 9252 10094 blaOXA-420 0/0 100.0 100.0 NG_049708.1 OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 CARBAPENEM
contig01773 33 848 blaOXA-60 0/0 100.0 100.0 NG_049800.1 carbapenem-hydrolyzing class D beta-lactamase OXA-60 CARBAPENEM
contig00966 1976 2341 ble-MBL 0/0 100.0 100.0 NG_047559.1 bleomycin binding protein Ble-MBL BLEOMYCIN
contig00812 696 1328 catB3 0/0 100.0 99.8 NG_047604.1 type B-3 chloramphenicol O-acetyltransferase CatB3 CHLORAMPHENICOL
contig00192 1187 2452 cmlB1 0/0 100.0 99.8 NG_047658.1 chloramphenicol efflux MFS transporter CmlB1 CHLORAMPHENICOL
contig01358 1213 1686 dfrA5 0/0 100.0 100.0 NG_051699.1 trimethoprim-resistant dihydrofolate reductase DfrA5 TRIMETHOPRIM
contig00785 1239 2453 floR 0/0 100.0 100.0 NG_047869.1 chloramphenicol/florfenicol efflux MFS transporter FloR CHLORAMPHENICOL, FLORFENICOL
contig01609 131 1052 mph(A) 1/1 100.0 99.6 NG_047986.1 Mph(A) family macrolide 2’-phosphotransferase MACROLIDE
contig00891 111 995 mph(E) 0/0 100.0 100.0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase MACROLIDE
contig00891 1051 2526 msr(E) 0/0 100.0 100.0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E) MACROLIDE
contig01714 93 932 sul1 0/0 100.0 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig01812 316 1128 sul2 0/0 99.6 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00971 143 1354 tet(31) 0/0 100.0 99.9 NG_048123.1 tetracycline efflux MFS transporter Tet(31) TETRACYCLINE
contig00474 867 2042 tet(G) 0/0 100.0 100.0 NG_051907.1 tetracycline efflux MFS transporter Tet(G) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01177 71 931 AAC3 0/0 100.0 100.0 MEG_64 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 NA
contig00154 13860 14662 ANT3-DPRIME 0/0 98.0 99.9 MEG_975 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00812 2377 3181 ANT3-DPRIME 0/0 96.9 99.8 MEG_915 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00474 3794 4621 APH3-DPRIME 0/0 100.0 100.0 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig01476 48 863 APH3-DPRIME 0/0 100.0 100.0 MEG_1044 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig02215 25 783 APH3-PRIME 0/0 97.3 100.0 MEG_1075 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-PRIME NA
contig00474 2958 3794 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00966 1976 2341 BRP 0/0 100.0 100.0 MEG_1477 Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP NA
contig00192 1187 2452 CMLB 0/0 100.0 99.8 MEG_1775 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:CMLB NA
contig01358 1213 1686 DFRA 0/0 100.0 100.0 MEG_2546 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00785 1239 2453 FLOR 0/0 100.0 100.0 MEG_2923 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR NA
contig01609 131 1052 MPHA 1/1 100.0 99.6 MEG_4030 Drugs:MLS:Macrolide_phosphotransferases:MPHA NA
contig00891 111 995 MPHE 0/0 100.0 100.0 MEG_4044 Drugs:MLS:Macrolide_phosphotransferases:MPHE NA
contig00891 1051 2526 MSRE 0/0 100.0 100.0 MEG_4075 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE NA
contig00966 1160 1972 NDM 0/0 100.0 100.0 MEG_4143 Drugs:betalactams:Class_B_betalactamases:NDM NA
contig00197 9225 10100 OXA 0/0 96.2 99.5 MEG_5259 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00812 1447 2277 OXA 0/0 100.0 100.0 MEG_4980 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig01290 1049 1838 OXA 0/0 95.8 99.9 MEG_4766 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig01773 33 848 OXA 0/0 100.0 100.0 MEG_4779 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig01358 691 1023 QACF 0/0 100.0 100.0 MEG_5838 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACF NA
contig01714 1 933 SULI 0/0 96.4 100.0 MEG_6615 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI NA
contig01812 316 1128 SULII 0/0 99.6 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00971 143 1375 TET31 0/0 100.0 100.0 MEG_6968 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET31 NA
contig00474 867 2042 TETG 0/0 100.0 100.0 MEG_7077 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETG NA
ID012II
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00060 1238 1771 ant(2’’)-Ia_1 0/0 100.0 100.0 X04555 ant(2’’)-Ia Gentamicin, Tobramycin
contig00052 3387 4189 aph(3’’)-Ib_2 0/0 99.9 100.0 AF024602 aph(3’’)-Ib Streptomycin
contig00060 372 1187 aph(3’)-Ia_7 0/0 100.0 100.0 X62115 aph(3’)-Ia
contig00052 2551 3387 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00001 9 1160 blaADC-25_1 0/0 100.0 99.9 EF016355 blaADC-25
contig00027 47 889 blaOXA-420_1 0/0 100.0 100.0 AB983359 blaOXA-420
contig00011 112601 113425 blaOXA-69_1 0/0 100.0 100.0 AY859527 blaOXA-69 Amoxicillin, Ampicillin
contig00040 21860 22369 dfrA20_1 0/0 100.0 100.0 AJ605332 dfrA20 Trimethoprim
contig00027 5534 6418 mph(E)_1 0/0 100.0 100.0 DQ839391 mph(E) Erythromycin
contig00027 6474 7949 msr(E)_1 0/0 100.0 100.0 FR751518 msr(E)
contig00063 277 1089 sul2_2 0/0 99.6 100.0 AY034138 sul2 Sulfamethoxazole
contig00027 11178 12299 tet(39)_1 0/0 100.0 100.0 KT346360 tet(39) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00006 14076 15422 abeM 0/0 100.0 98.9 AB204810:186-1533 AbeM is an multidrug efflux pump found in Acinetobacter baumannii. acridine_dye, fluoroquinolone, triclosan
contig00009 77409 77738 abeS 0/0 100.0 100.0 CP001172.1:1249348-1249018 AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. aminocoumarin, macrolide
contig00029 28006 29295 Acinetobacter_baumannii_AbaF 0/0 100.0 97.9 CP000521.1:1558523-1557233 Expression of abaF in E. coli resulted in increased resistance to fosfomycin. fosfomycin
contig00012 20581 21885 Acinetobacter_baumannii_AbaQ 0/0 100.0 100.0 CP001182.2:2256889-2255584 AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii fluoroquinolone
contig00008 19900 21378 Acinetobacter_baumannii_AmvA 0/0 100.0 100.0 FJ911554.1:176-1655 AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. acridine_dye, macrolide
contig00001 9 1160 ADC-30 0/0 100.0 100.0 JF265068.1:954-2106 An ADC beta-lactamase and cephalosporinase from Acinetobacter baumannii cephalosporin
contig00031 12186 13376 adeA 0/0 100.0 97.7 AF370885.1:3438-4629 AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. glycylcycline, tetracycline
contig00031 9079 12186 adeB 0/0 100.0 97.8 AF370885.1:4628-7736 AdeB is the multidrug transporter of the adeABC efflux system. glycylcycline, tetracycline
contig00031 7605 9002 adeC 0/0 100.0 95.4 CP013924.1:2063742-2065140 AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. glycylcycline, tetracycline
contig00009 68465 71644 adeF 0/0 100.0 100.0 CT025801.2:0-3180 AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. fluoroquinolone, tetracycline
contig00009 71651 72871 adeG 0/0 100.0 100.0 CT025800.2:0-1221 AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00009 67004 68455 adeH 0/0 100.0 100.0 CT025802.2:0-1452 AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00017 41693 42943 adeI 0/0 100.0 100.0 CP001182.2:3283426-3284677 AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00017 42956 46132 adeJ 0/0 100.0 99.6 AY769962:2434-5611 AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00017 46132 47586 adeK 0/0 100.0 98.7 AY769962:5610-7065 AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00009 73087 74100 adeL 0/0 100.0 99.4 KR297239.1:1428-414 AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. fluoroquinolone, tetracycline
contig00008 75439 76092 adeN 0/0 100.0 98.0 KF147862:0-654 AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00031 13522 14265 adeR 0/0 100.0 100.0 HM440348:0-744 AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. glycylcycline, tetracycline
contig00031 14297 15382 adeS 0/0 100.0 99.7 HM440348:775-1861 AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. glycylcycline, tetracycline
contig00060 1238 1771 ANT(2’’)-Ia 0/0 100.0 100.0 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00052 3387 4190 APH(3’’)-Ib 0/0 100.0 99.9 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00060 372 1187 APH(3’)-Ia 0/0 100.0 100.0 BX664015.1:103833-103017 APH(3’)-Ia is a transposon-encoded aminoglycoside phosphotransferase in E. coli and S. enterica. It is identical at the protein sequence to APH(3’)-Ic an aminoglycoside phosphotransferase encoded by plasmids transposons and genomic islands in K. pneumoniae A. baumannii S. marcescens Corynebacterium spp. Photobacterium spp. and Citrobacter spp. aminoglycoside
contig00052 2551 3387 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00040 21860 22369 dfrA20 0/0 100.0 100.0 AJ605332:1303-1813 dfrA20 is a plasmid-encoded dihydrofolate reductase found in Pasteurella multocida diaminopyrimidine
contig00027 5534 6418 mphE 0/0 100.0 100.0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 macrolide
contig00027 6474 7949 msrE 0/0 100.0 100.0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00027 47 889 OXA-420 0/0 100.0 100.0 AB983359:2425-3268 From the Lahey list of beta-lactamases. Not yet released. cephalosporin, penam
contig00011 112601 113425 OXA-69 0/0 100.0 100.0 CU459141.1:2175316-2176141 OXA-69 is a beta-lactamase found in A. baumannii cephalosporin, penam
contig00063 277 1089 sul2 0/0 99.6 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00027 11112 12299 tet(39) 0/0 100.0 100.0 AY743590:0-1188 Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00060 1238 1771 (AGly)aadB 0/0 100.0 100.0 JQ690540:4275-4808 (AGly)aadB NA
contig00025 23905 24693 (AGly)ant(3’’)-IIa 0/0 100.0 98.9 NG_054648:101-889 (AGly)ant(3’’)-IIa NA
contig00060 372 1187 (AGly)aph(3’’)-Ia 0/0 100.0 100.0 FJ172370:38668-39483 (AGly)aph(3’’)-Ia NA
contig00052 3387 4190 (AGly)strA 0/0 100.0 100.0 AB366441:22458-23261 (AGly)strA NA
contig00052 2551 3387 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00012 7956 8975 (Bla)BlaA1 0/0 100.0 99.9 NC_010410:1803480-1804499 (Bla)BlaA1 NA
contig00022 41824 43098 (Bla)BlaA2 0/0 100.0 100.0 NC_010410:2507740-2509014 (Bla)BlaA2 NA
contig00001 9 1160 (Bla)blaADC-30 0/0 100.0 100.0 JF265068:955-2106 (Bla)blaADC-30 NA
contig00027 47 889 (Bla)blaOXA-58 0/0 100.0 99.6 AY665723:3301-4143 (Bla)blaOXA-58 NA
contig00011 112601 113425 (Bla)blaOXA-69 0/0 100.0 100.0 AY750911:1-825 (Bla)blaOXA-69 NA
contig00007 31147 31842 (Bla)Mbl 0/0 100.0 100.0 NC_010410:c1997136-1996441 (Bla)Mbl NA
contig00001 314995 315957 (Bla)Zn-dependent_hydrolase 0/0 100.0 100.0 NC_010410:882015-882977 (Bla)Zn-dependent_hydrolase NA
contig00027 5534 6418 (MLS)mph(E) 0/0 100.0 99.9 JF769133:8777-9661 (MLS)mph(E) NA
contig00027 6474 7949 (MLS)msr(E) 0/0 100.0 100.0 JF769133:7246-8721 (MLS)msr(E) NA
contig00063 277 1089 (Sul)sul2 0/0 99.6 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00027 11112 12299 (Tet)tet(39) 0/0 100.0 100.0 AY743590:749-1936 (Tet)tet(39) NA
contig00040 21860 22369 (Tmt)dfrA20 0/0 100.0 100.0 AJ605332:1304-1813 (Tmt)dfrA20 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00060 1238 1771 ant(2’’)-Ia 0/0 100.0 100.0 NG_047387.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00025 23905 24693 ant(3’’)-IIa 0/0 100.0 100.0 NG_054646.1 aminoglycoside nucleotidyltransferase ANT(3’’)-IIa SPECTINOMYCIN, STREPTOMYCIN
contig00052 3387 4214 aph(3’’)-Ib 0/0 100.0 99.9 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00060 372 1187 aph(3’)-Ia 0/0 100.0 100.0 NG_047431.1 aminoglycoside O-phosphotransferase APH(3’)-Ia KANAMYCIN
contig00052 2551 3387 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00001 9 1160 blaADC-30 0/0 100.0 100.0 NG_048652.1 class C extended-spectrum beta-lactamase ADC-30 CEPHALOSPORIN
contig00027 47 889 blaOXA-420 0/0 100.0 100.0 NG_049708.1 OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 CARBAPENEM
contig00011 112601 113425 blaOXA-69 0/0 100.0 100.0 NG_049809.1 OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 CARBAPENEM
contig00040 21860 22369 dfrA20 0/0 100.0 100.0 NG_047714.1 trimethoprim-resistant dihydrofolate reductase DfrA20 TRIMETHOPRIM
contig00027 5534 6418 mph(E) 0/0 100.0 100.0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase MACROLIDE
contig00027 6474 7949 msr(E) 0/0 100.0 100.0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E) MACROLIDE
contig00063 277 1089 sul2 0/0 99.6 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00027 11112 12299 tet(39) 0/0 100.0 100.0 NG_048137.1 tetracycline efflux MFS transporter Tet(39) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00029 28006 29295 ABAF 0/0 100.0 97.9 MEG_369 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF NA
contig00012 20581 21885 ABAQ 0/0 100.0 100.0 MEG_370 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ NA
contig00006 14076 15422 ABEM 0/0 100.0 98.9 MEG_372 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM NA
contig00009 77409 77738 ABES 0/0 100.0 100.0 MEG_379 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES NA
contig00001 9 1160 ADC 0/0 100.0 100.0 MEG_658 Drugs:betalactams:Class_C_betalactamases:ADC NA
contig00031 12186 13376 ADEA 0/0 100.0 97.7 MEG_677 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA NA
contig00031 9079 12186 ADEB 0/0 100.0 97.8 MEG_678 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB NA
contig00031 7605 9002 ADEC 0/0 100.0 95.4 MEG_679 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC NA
contig00009 71651 72871 ADEF 0/0 100.0 100.0 MEG_683 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF NA
contig00009 68465 71644 ADEG 0/0 100.0 100.0 MEG_684 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG NA
contig00009 67004 68455 ADEH 0/0 100.0 100.0 MEG_685 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH NA
contig00017 41693 42943 ADEI 0/0 100.0 100.0 MEG_686 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI NA
contig00017 42956 46132 ADEJ 0/0 100.0 99.6 MEG_692 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ NA
contig00017 46132 47586 ADEK 0/0 100.0 99.0 MEG_696 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK NA
contig00009 73087 74100 ADEL 0/0 100.0 99.5 MEG_699 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL NA
contig00008 75439 76092 ADEN 0/0 100.0 100.0 MEG_701 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN NA
contig00031 13522 14265 ADER 0/0 100.0 100.0 MEG_703 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER NA
contig00031 14297 15382 ADES 0/0 100.0 99.7 MEG_704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES NA
contig00016 50011 50727 ADET2 0/0 100.0 98.9 MEG_706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 NA
contig00008 19900 21378 AMVA 0/0 100.0 100.0 MEG_733 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA NA
contig00025 23905 24693 ANT3-DPRIME 0/0 100.0 100.0 MEG_913 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00052 3387 4214 APH3-DPRIME 0/0 100.0 99.9 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00060 372 1187 APH3-DPRIME 0/0 100.0 100.0 MEG_1044 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00052 2551 3387 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00012 7956 8975 BLAA 0/0 100.0 99.9 MEG_1246 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00022 41824 43098 BLAA 0/0 100.0 100.0 MEG_1247 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00034 25919 26908 MEXT 0/0 100.0 98.8 MEG_3934 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT NA
contig00027 5534 6418 MPHE 0/0 100.0 100.0 MEG_4044 Drugs:MLS:Macrolide_phosphotransferases:MPHE NA
contig00027 6474 7949 MSRE 0/0 100.0 100.0 MEG_4075 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE NA
contig00011 112556 113507 OXA 3/3 98.9 97.5 MEG_5236 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00027 41 916 OXA 0/0 96.2 99.5 MEG_5259 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00063 277 1089 SULII 0/0 99.6 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00027 11112 12299 TET39 0/0 100.0 100.0 MEG_6987 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 NA
ID014II
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00373 2685 3545 aac(3)-IId_1 0/0 100.0 99.9 EU022314 aac(3)-IId Gentamicin, Tobramycin
contig00373 1272 2074 aph(3’’)-Ib_2 0/0 99.9 100.0 AF024602 aph(3’’)-Ib Streptomycin
contig00373 436 1272 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00414 1262 2137 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00473 93 905 blaNDM-1_1 0/0 100.0 100.0 FN396876 blaNDM-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00052 35257 36087 blaOXA-356_1 0/0 100.0 100.0 KF297585 blaOXA-356
contig00445 878 1720 blaOXA-420_1 0/0 100.0 100.0 AB983359 blaOXA-420
contig00411 1004 1663 catA1_1 0/0 100.0 99.8 V00622 catA1 Chloramphenicol
contig00465 134 631 dfrA12_8 0/0 100.0 100.0 AM040708 dfrA12 Trimethoprim
contig00425 327 1540 floR_2 0/0 99.9 98.3 AF118107 floR Chloramphenicol, Florfenicol
contig00079 22839 24071 mdf(A)_1 0/0 100.0 99.9 Y08743 mdf(A)
contig00395 121 1005 mph(E)_1 0/0 100.0 100.0 DQ839391 mph(E) Erythromycin
contig00395 1061 2536 msr(E)_1 0/0 100.0 100.0 FR751518 msr(E)
contig00396 972 1838 sul1_5 0/0 100.0 99.9 EU780013 sul1 Sulfamethoxazole
contig00391 328 1143 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00424 82 1203 tet(39)_1 0/0 100.0 99.9 KT346360 tet(39) Doxycycline, Tetracycline
contig00394 948 2153 tet(B)_2 0/0 100.0 100.0 AF326777 tet(B) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00373 2685 3545 AAC(3)-IId 0/0 100.0 99.9 EU022314.1:0-861 AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig00090 26373 29522 acrB 0/0 100.0 100.0 U00096.3:484403-481253 Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00048 38923 42036 acrD 0/0 100.0 100.0 AP009048.1:2586250-2589364 AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. aminoglycoside
contig00056 7448 8605 acrE 0/0 100.0 99.9 U00096:3413863-3415021 AcrE is a membrane fusion protein similar to AcrA. cephalosporin, cephamycin, fluoroquinolone, penam
contig00056 4332 7436 acrF 0/0 100.0 99.9 U00096:3415032-3418137 AcrF is a inner membrane transporter similar to AcrB. cephalosporin, cephamycin, fluoroquinolone, penam
contig00056 9004 9666 acrS 0/0 100.0 100.0 U00096:3413465-3412802 AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux. cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00373 1272 2075 APH(3’’)-Ib 0/0 100.0 99.9 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00373 436 1272 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00374 1375 2196 bacA 0/0 100.0 98.7 U00096.3:3204131-3203309 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. peptide
contig00225 7328 8050 baeR 0/0 100.0 99.5 AP009048.1:2166412-2167135 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. aminocoumarin, aminoglycoside
contig00225 5928 7331 baeS 0/0 100.0 99.9 AP009048:2165012-2166416 BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance. aminocoumarin, aminoglycoside
contig00411 1004 1663 catI 0/0 100.0 99.8 V00622:243-903 catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii phenicol
contig00028 30399 31772 cpxA 0/0 100.0 99.0 BA000007.3:4905062-4903688 CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. aminocoumarin, aminoglycoside
contig00083 15080 15712 CRP 0/0 100.0 99.4 AP009048.1:4154296-4153663 CRP is a global regulator that represses MdtEF multidrug efflux pump expression. fluoroquinolone, macrolide, penam
contig00414 1262 2137 CTX-M-15 0/0 100.0 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig00473 909 1243 determinant_of_bleomycin_resistance 0/0 91.5 100.0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide
contig00465 134 631 dfrA12 0/0 100.0 100.0 GU585907.1:22103-21605 dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine
contig00217 1578 2750 emrA 0/0 100.0 100.0 AP009048:2810082-2811255 EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. fluoroquinolone
contig00217 23 1561 emrB 0/0 100.0 100.0 U00096:2812615-2814154 emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. fluoroquinolone
contig00021 62059 63114 emrK 0/0 100.0 99.9 D78168:536-1592 emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux. tetracycline
contig00217 2877 3407 emrR 0/0 100.0 99.8 U00096.3:2810769-2811300 EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. fluoroquinolone
contig00021 60521 62059 emrY 0/0 100.0 99.9 D78168:1591-3130 emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. tetracycline
contig00101 7608 9251 eptA 0/0 100.0 99.9 AP009048:4340268-4338624 PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B. peptide
contig00244 2156 3289 Escherichia_coli_ampC 0/0 100.0 97.3 U00096.3:4378944-4377810 A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. cephalosporin, penam
contig00125 17231 18535 Escherichia_coli_ampC1_beta-lactamase 0/0 100.0 99.9 FN649414.1:2765050-2766355 An ampC-like beta-lactamase identified from Escherichia coli. cephalosporin, penam
contig00150 4921 6078 Escherichia_coli_ampH 0/0 100.0 100.0 AP012030.1:396711-395553 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. cephalosporin, penam
contig00079 22839 24071 Escherichia_coli_mdfA 0/0 100.0 98.4 JQ394987:0-1233 Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. benzalkonium_chloride, rhodamine, tetracycline
contig00021 63637 64251 evgA 0/0 100.0 100.0 BA000007.3:3212025-3212640 EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed. fluoroquinolone, macrolide, penam, tetracycline
contig00021 64256 67849 evgS 0/0 100.0 100.0 U00096:2484373-2487967 EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. fluoroquinolone, macrolide, penam, tetracycline
contig00425 326 1540 floR 0/0 100.0 99.9 AF231986:3307-4522 floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae phenicol
contig00067 1220 1948 gadW 0/0 100.0 94.7 CP015085.1:2552440-2551711 GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC. fluoroquinolone, macrolide, penam
contig00067 29 853 gadX 0/0 100.0 100.0 AP009048.1:3974604-3975429 GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. fluoroquinolone, macrolide, penam
contig00334 4348 4761 H-NS 0/0 100.0 99.3 BA000007.3:1738104-1737690 H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00084 7616 8293 kdpE 0/0 100.0 100.0 U00096.3:721733-721055 kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. aminoglycoside
contig00242 1239 1622 marA 0/0 100.0 100.0 AP009048.1:1621287-1621671 In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00377 554 1801 mdtA 0/0 100.0 98.0 U00096:2154015-2155263 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. aminocoumarin
contig00225 1438 4515 mdtC 0/0 100.0 99.9 U00096:2158385-2161463 MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. aminocoumarin
contig00067 5449 6606 mdtE 0/0 100.0 100.0 AP009048.1:3981183-3980025 MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. fluoroquinolone, macrolide, penam
contig00067 2311 5424 mdtF 0/0 100.0 100.0 U00096:3660413-3663527 MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. fluoroquinolone, macrolide, penam
contig00298 1763 2989 mdtG 0/0 100.0 99.3 CP000800.1:1192954-1191727 The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon. fosfomycin
contig00306 3604 4812 mdtH 0/0 100.0 100.0 U00096:1125326-1124117 Multidrug resistance protein MdtH fluoroquinolone
contig00100 473 1684 mdtM 0/0 98.3 95.5 U00096.3:4568519-4567286 Multidrug resistance protein MdtM acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00114 17480 18511 mdtN 0/0 100.0 100.0 AP009048.1:4307588-4306556 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. acridine_dye, nucleoside
contig00114 15429 17480 mdtO 0/0 100.0 100.0 AP009048.1:4306557-4304505 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride acridine_dye, nucleoside
contig00114 13966 15432 mdtP 0/0 100.0 100.0 AP009048.1:4304509-4303042 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride acridine_dye, nucleoside
contig00048 17761 18237 mphB 0/0 100.0 98.3 AE005174.2:3397370-3397847 The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides. macrolide
contig00395 121 1005 mphE 0/0 100.0 100.0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 macrolide
contig00127 520 2268 msbA 0/0 100.0 100.0 U00096.3:966620-968369 MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. nitroimidazole
contig00395 1061 2536 msrE 0/0 100.0 100.0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00473 93 905 NDM-1 0/0 100.0 100.0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. carbapenem, cephalosporin, cephamycin, penam
contig00052 35257 36087 OXA-356 0/0 100.0 100.0 KF297585:0-831 OXA-356 is a beta-lactamase. From the Lahey list of OXA beta-lactamases. cephalosporin, penam
contig00445 878 1720 OXA-420 0/0 100.0 100.0 AB983359:2425-3268 From the Lahey list of beta-lactamases. Not yet released. cephalosporin, penam
contig00115 5199 6167 pmrF 0/0 100.0 100.0 U00096:2367070-2368039 PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. peptide
contig00396 972 1811 sul1 0/0 100.0 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00391 328 1143 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00424 82 1269 tet(39) 0/0 100.0 99.9 AY743590:0-1188 Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. tetracycline
contig00394 948 2153 tet(B) 0/0 100.0 99.8 AB089595:0-1206 Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline. tetracycline
contig00069 15133 16620 tolC 0/0 100.0 99.7 FJ768952:0-1488 TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00198 9354 10997 yojI 0/0 100.0 100.0 U00096.3:2308615-2306971 YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. peptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00373 2685 3545 (AGly)aac3-IId 0/0 100 99.9 EU022314:1-861 (AGly)aac3-IId NA
contig00373 1272 2075 (AGly)strA 0/0 100 100.0 AB366441:22458-23261 (AGly)strA NA
contig00373 436 1272 (AGly)strB 0/0 100 100.0 FJ474091:264-1100 (AGly)strB NA
contig00125 17231 18535 (Bla)AmpC1_Ecoli 0/0 100 99.9 FN649414:2765051-2766355 (Bla)AmpC1_Ecoli NA
contig00244 2156 3289 (Bla)AmpC2_Ecoli 0/0 100 97.3 CP002970:332756-333889 (Bla)AmpC2_Ecoli NA
contig00150 4921 6078 (Bla)ampH_Ecoli 0/0 100 100.0 AP012030:395554-396711 (Bla)ampH_Ecoli NA
contig00414 1262 2137 (Bla)blaCTX-M-15 0/0 100 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig00473 93 905 (Bla)blaNDM-1 0/0 100 100.0 JQ080305:1-813 (Bla)blaNDM-1 NA
contig00052 35257 36087 (Bla)blaOXA-230 0/0 100 99.0 JQ422054:101-931 (Bla)blaOXA-230 NA
contig00445 878 1720 (Bla)blaOXA-58 0/0 100 99.6 AY665723:3301-4143 (Bla)blaOXA-58 NA
contig00258 5144 7045 (Bla)Penicillin_Binding_Protein_Ecoli 0/0 100 100.0 CP002291:664439-666340 (Bla)Penicillin_Binding_Protein_Ecoli NA
contig00395 121 1005 (MLS)mph(E) 0/0 100 99.9 JF769133:8777-9661 (MLS)mph(E) NA
contig00395 1061 2536 (MLS)msr(E) 0/0 100 100.0 JF769133:7246-8721 (MLS)msr(E) NA
contig00411 1004 1663 (Phe)catA1 0/0 100 99.8 V00622:244-903 (Phe)catA1 NA
contig00425 326 1540 (Phe)floR 0/0 100 99.8 AKLJ01000508:383-1597 (Phe)floR NA
contig00396 972 1811 (Sul)sul1 0/0 100 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig00391 328 1143 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00424 82 1269 (Tet)tet(39) 0/0 100 99.9 AY743590:749-1936 (Tet)tet(39) NA
contig00394 948 2153 (Tet)tetB 0/0 100 99.7 AB089594:1-1206 (Tet)tetB NA
contig00465 134 631 (Tmt)dfrA12 0/0 100 100.0 Z21672:310-807 (Tmt)dfrA12 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00373 2685 3545 aac(3)-IId 0/0 100.0 100.0 NG_047251.1 aminoglycoside N-acetyltransferase AAC(3)-IId GENTAMICIN
contig00373 1272 2099 aph(3’’)-Ib 0/0 100.0 99.9 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00373 436 1272 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00414 1262 2137 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00244 2156 3289 blaEC-15 0/0 100.0 98.5 NG_049081.1 class C extended-spectrum beta-lactamase EC-15 CEPHALOSPORIN
contig00473 93 905 blaNDM-1 0/0 100.0 100.0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1 CARBAPENEM
contig00052 35257 36087 blaOXA-356 0/0 100.0 100.0 NG_049649.1 OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-356 CARBAPENEM
contig00445 878 1720 blaOXA-420 0/0 100.0 100.0 NG_049708.1 OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 CARBAPENEM
contig00473 909 1243 ble-MBL 0/0 91.5 100.0 NG_047559.1 bleomycin binding protein Ble-MBL BLEOMYCIN
contig00411 1004 1663 catA1 0/0 100.0 99.8 NG_047582.1 type A-1 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00465 134 631 dfrA12 0/0 100.0 100.0 NG_047689.1 trimethoprim-resistant dihydrofolate reductase DfrA12 TRIMETHOPRIM
contig00425 326 1540 floR 0/0 100.0 100.0 NG_047869.1 chloramphenicol/florfenicol efflux MFS transporter FloR CHLORAMPHENICOL, FLORFENICOL
contig00395 121 1005 mph(E) 0/0 100.0 100.0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase MACROLIDE
contig00395 1061 2536 msr(E) 0/0 100.0 100.0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E) MACROLIDE
contig00396 972 1811 sul1 0/0 100.0 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig00391 328 1143 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00424 82 1269 tet(39) 0/0 100.0 99.9 NG_048137.1 tetracycline efflux MFS transporter Tet(39) TETRACYCLINE
contig00394 948 2153 tet(B) 0/0 100.0 100.0 NG_048163.1 tetracycline efflux MFS transporter Tet(B) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00373 2685 3545 AAC3 0/0 100.0 100.0 MEG_64 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 NA
contig00090 26373 29522 ACRB 0/0 100.0 100.0 MEG_401 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB NA
contig00048 38923 42036 ACRD 0/0 100.0 100.0 MEG_407 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD NA
contig00056 7448 8605 ACRE 0/0 100.0 99.9 MEG_408 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE NA
contig00056 4332 7436 ACRF 0/0 100.0 99.9 MEG_409 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF NA
contig00056 9004 9666 ACRS 0/0 100.0 100.0 MEG_415 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS NA
contig00150 4921 6078 AMPH 0/0 100.0 100.0 MEG_729 Drugs:betalactams:Penicillin_binding_protein:AMPH NA
contig00373 1272 2099 APH3-DPRIME 0/0 100.0 99.9 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00373 436 1272 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00156 2787 4639 ASMA 0/0 100.0 97.2 MEG_1180 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA NA
contig00374 1375 2196 BACA 0/0 100.0 98.9 MEG_1189 Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA NA
contig00225 7328 8050 BAER 0/0 100.0 99.5 MEG_1192 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER NA
contig00225 5928 7331 BAES 0/0 100.0 99.9 MEG_1193 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES NA
contig00080 9933 11123 BCR 0/0 100.0 99.9 MEG_1210 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR NA
contig00244 2156 3289 BLAEC 0/0 100.0 98.5 MEG_1282 Drugs:betalactams:Class_C_betalactamases:BLAEC NA
contig00473 909 1243 BRP 0/0 91.5 100.0 MEG_1477 Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP NA
contig00411 999 1663 CATA 0/0 99.1 100.0 MEG_1593 Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA NA
contig00028 29704 30402 CPXAR 0/0 100.0 100.0 MEG_2122 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR NA
contig00028 30399 31772 CPXAR 0/0 100.0 100.0 MEG_2121 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR NA
contig00083 15080 15712 CRP 0/0 100.0 99.4 MEG_2132 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP NA
contig00160 13705 14647 CTX 0/0 100.0 98.2 MEG_2435 Drugs:betalactams:Class_A_betalactamases:CTX NA
contig00465 134 631 DFRA 0/0 100.0 100.0 MEG_2551 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00217 1578 2750 EMRA 0/0 100.0 100.0 MEG_2722 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA NA
contig00217 23 1561 EMRB 0/0 100.0 100.0 MEG_2725 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB NA
contig00120 19649 20839 EMRD 0/0 100.0 99.9 MEG_2729 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD NA
contig00021 62059 63222 EMRK 0/0 100.0 99.9 MEG_2732 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK NA
contig00217 2877 3407 EMRR 0/0 100.0 99.8 MEG_2734 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR NA
contig00021 60521 62059 EMRY 0/0 100.0 99.9 MEG_2736 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY NA
contig00101 7608 9251 EPTA 0/0 100.0 99.9 MEG_2739 Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA NA
contig00021 64256 67849 EVGS 0/0 100.0 100.0 MEG_2870 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS NA
contig00425 326 1540 FLOR 0/0 100.0 100.0 MEG_2923 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR NA
contig00067 1220 1948 GADW 0/0 100.0 100.0 MEG_3081 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW NA
contig00067 29 853 GADX 0/0 100.0 100.0 MEG_3083 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX NA
contig00334 4348 4761 HNS 0/0 100.0 99.3 MEG_3271 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS NA
contig00084 7616 8293 KDPE 0/0 100.0 100.0 MEG_3448 Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE NA
contig00242 1233 1622 MARA 0/0 100.0 100.0 MEG_3662 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA NA
contig00242 785 1219 MARR 0/0 100.0 100.0 MEG_3663 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR NA
contig00079 22839 24071 MDFA 0/0 100.0 100.0 MEG_3737 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA NA
contig00377 554 1801 MDTA 0/0 100.0 98.0 MEG_3746 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA NA
contig00225 1438 4515 MDTC 0/0 100.0 99.9 MEG_3749 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC NA
contig00067 5449 6606 MDTE 0/0 100.0 100.0 MEG_3751 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE NA
contig00067 2311 5424 MDTF 0/0 100.0 100.0 MEG_3752 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF NA
contig00298 1763 2989 MDTG 0/0 100.0 99.9 MEG_3753 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG NA
contig00306 3604 4812 MDTH 0/0 100.0 100.0 MEG_3755 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH NA
contig00043 23790 24119 MDTI 0/0 100.0 100.0 MEG_3756 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI NA
contig00043 24106 24471 MDTJ 0/0 100.0 99.5 MEG_3757 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ NA
contig00182 11709 13082 MDTK 0/0 100.0 100.0 MEG_3759 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK NA
contig00100 473 1684 MDTM 0/0 98.3 95.5 MEG_3761 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM NA
contig00114 17480 18511 MDTN 0/0 100.0 100.0 MEG_3763 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN NA
contig00114 15429 17480 MDTO 0/0 100.0 100.0 MEG_3764 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO NA
contig00114 13966 15432 MDTP 0/0 100.0 100.0 MEG_3765 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP NA
contig00048 17761 18237 MPHB 0/0 100.0 98.3 MEG_4033 Drugs:MLS:Macrolide_phosphotransferases:MPHB NA
contig00395 121 1005 MPHE 0/0 100.0 100.0 MEG_4044 Drugs:MLS:Macrolide_phosphotransferases:MPHE NA
contig00127 520 2268 MSBA 0/0 100.0 100.0 MEG_4061 Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA NA
contig00395 1061 2536 MSRE 0/0 100.0 100.0 MEG_4075 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE NA
contig00473 93 905 NDM 0/0 100.0 100.0 MEG_4143 Drugs:betalactams:Class_B_betalactamases:NDM NA
contig00052 35222 36187 OXA 0/0 100.0 98.9 MEG_5220 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00445 872 1742 OXA 0/0 95.6 99.5 MEG_5259 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00258 5144 7045 PBP2 0/0 100.0 100.0 MEG_5400 Drugs:betalactams:Penicillin_binding_protein:PBP2 NA
contig00125 17231 18535 PBP4B 0/0 100.0 99.9 MEG_5409 Drugs:betalactams:Penicillin_binding_protein:PBP4B NA
contig00115 5199 6167 PMRF 0/0 100.0 100.0 MEG_5801 Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF NA
contig00065 2810 3679 ROBA 0/0 100.0 99.0 MEG_6082 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA NA
contig00238 2432 2755 SOXS 0/0 100.0 100.0 MEG_6551 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS NA
contig00396 845 1812 SULI 0/0 100.0 100.0 MEG_6615 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI NA
contig00391 328 1143 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00424 82 1269 TET39 0/0 100.0 99.9 MEG_6987 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 NA
contig00394 948 2153 TETB 0/0 100.0 100.0 MEG_7052 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB NA
contig00198 9354 10997 YOGI 0/0 100.0 100.0 MEG_7842 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI NA
ID030
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00231 4721 5254 ant(2’’)-Ia_13 0/0 100.0 99.1 DQ176450 ant(2’’)-Ia Gentamicin, Tobramycin
contig00184 6719 7521 aph(3’’)-Ib_2 0/0 99.9 100.0 AF024602 aph(3’’)-Ib Streptomycin
contig00184 5883 6719 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00968 92 904 blaNDM-1_1 0/0 100.0 100.0 FN396876 blaNDM-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00614 1050 1874 blaOXA-22_1 0/0 100.0 100.0 AF064820 blaOXA-22 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00525 254 1096 blaOXA-420_1 0/0 100.0 100.0 AB983359 blaOXA-420
contig01193 1 803 blaOXA-60_1 0/0 98.4 100.0 AF525303 blaOXA-60 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem
contig01103 503 1318 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00231 4721 5254 ANT(2’’)-Ia 0/0 100.0 98.9 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00184 6719 7522 APH(3’’)-Ib 0/0 100.0 99.9 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00184 5883 6719 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00968 908 1273 determinant_of_bleomycin_resistance 0/0 100.0 100.0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide
contig00968 92 904 NDM-1 0/0 100.0 100.0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. carbapenem, cephalosporin, cephamycin, penam
contig00614 1050 1874 OXA-22 0/0 100.0 100.0 AF064820:951-1776 OXA-22 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig00525 254 1096 OXA-420 0/0 100.0 100.0 AB983359:2425-3268 From the Lahey list of beta-lactamases. Not yet released. cephalosporin, penam
contig01193 1 803 OXA-60 0/0 98.4 100.0 AF525303:2770-3586 OXA-60 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig01103 503 1318 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00231 4721 5254 (AGly)aadB 0/0 100.0 98.9 JQ690540:4275-4808 (AGly)aadB NA
contig00184 6719 7522 (AGly)strA 0/0 100.0 100.0 AB366441:22458-23261 (AGly)strA NA
contig00184 5883 6719 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00968 92 904 (Bla)blaNDM-1 0/0 100.0 100.0 JQ080305:1-813 (Bla)blaNDM-1 NA
contig00614 1050 1874 (Bla)blaOXA-22 0/0 100.0 100.0 AF064820:952-1776 (Bla)blaOXA-22 NA
contig00525 254 1096 (Bla)blaOXA-58 0/0 100.0 99.6 AY665723:3301-4143 (Bla)blaOXA-58 NA
contig01193 3 803 (Bla)blaOXA-60 0/0 98.2 93.5 AY664505:1-816 (Bla)blaOXA-60 NA
contig01103 503 1318 (Sul)sul2 0/0 100.0 100.0 EU360945:1617-2432 (Sul)sul2 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00231 4721 5254 ant(2’’)-Ia 0/0 100.0 99.1 NG_052432.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00184 6719 7546 aph(3’’)-Ib 0/0 100.0 99.9 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00184 5883 6719 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00968 92 904 blaNDM-1 0/0 100.0 100.0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1 CARBAPENEM
contig00614 1050 1874 blaOXA-22 0/0 100.0 100.0 NG_049518.1 benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 BETA-LACTAM
contig00525 254 1096 blaOXA-420 0/0 100.0 100.0 NG_049708.1 OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 CARBAPENEM
contig01193 1 803 blaOXA-60 0/0 98.4 100.0 NG_049800.1 carbapenem-hydrolyzing class D beta-lactamase OXA-60 CARBAPENEM
contig00968 908 1273 ble-MBL 0/0 100.0 100.0 NG_047559.1 bleomycin binding protein Ble-MBL BLEOMYCIN
contig01103 503 1318 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00184 6719 7546 APH3-DPRIME 0/0 100.0 99.9 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00184 5883 6719 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00968 908 1273 BRP 0/0 100.0 100.0 MEG_1477 Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP NA
contig00968 92 904 NDM 0/0 100.0 100.0 MEG_4143 Drugs:betalactams:Class_B_betalactamases:NDM NA
contig00525 227 1102 OXA 0/0 96.2 99.5 MEG_5259 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00614 1050 1874 OXA 0/0 100.0 100.0 MEG_4766 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig01193 1 803 OXA 0/0 98.4 100.0 MEG_4779 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig01103 503 1318 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
ID063
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00046 23105 23908 aph(3’’)-Ib_5 0/0 100.0 100.0 AF321551 aph(3’’)-Ib Streptomycin
contig00046 22269 23105 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00046 16991 17866 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00046 20688 21548 blaTEM-1B_1 0/0 100.0 100.0 AY458016 blaTEM-1B Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00086 182 664 dfrA14_5 0/0 100.0 99.6 DQ388123 dfrA14 Trimethoprim
contig00044 26094 27326 mdf(A)_1 0/0 100.0 99.9 Y08743 mdf(A)
contig00046 11694 12350 qnrS1_1 0/0 100.0 100.0 AB187515 qnrS1 Ciprofloxacin
contig00046 23969 24784 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00072 2413 3659 tet(A)_6 0/0 97.8 100.0 AF534183 tet(A) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 39911 43060 acrB 0/0 100.0 100.0 U00096.3:484403-481253 Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00001 264252 267365 acrD 0/0 100.0 100.0 AP009048.1:2586250-2589364 AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. aminoglycoside
contig00033 8847 10004 acrE 0/0 100.0 100.0 U00096:3413863-3415021 AcrE is a membrane fusion protein similar to AcrA. cephalosporin, cephamycin, fluoroquinolone, penam
contig00033 5731 8835 acrF 0/0 100.0 99.5 U00096:3415032-3418137 AcrF is a inner membrane transporter similar to AcrB. cephalosporin, cephamycin, fluoroquinolone, penam
contig00033 10403 11065 acrS 0/0 100.0 100.0 U00096:3413465-3412802 AcrS is a repressor of the AcrAB efflux complex and is associated with the expression of AcrEF. AcrS is believed to regulate a switch between AcrAB and AcrEF efflux. cephalosporin, cephamycin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00046 23105 23908 APH(3’’)-Ib 0/0 100.0 99.8 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00046 22269 23105 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00043 29802 30623 bacA 0/0 100.0 100.0 U00096.3:3204131-3203309 The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. peptide
contig00002 136446 137168 baeR 0/0 100.0 100.0 AP009048.1:2166412-2167135 BaeR is a response regulator that promotes the expression of MdtABC and AcrD efflux complexes. aminocoumarin, aminoglycoside
contig00002 137165 138568 baeS 0/0 100.0 100.0 AP009048:2165012-2166416 BaeS is a sensor kinase in the BaeSR regulatory system. While it phosphorylates BaeR to increase its activity BaeS is not necessary for overexpressed BaeR to confer resistance. aminocoumarin, aminoglycoside
contig00037 2729 4102 cpxA 0/0 100.0 99.0 BA000007.3:4905062-4903688 CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. aminocoumarin, aminoglycoside
contig00045 15323 15955 CRP 0/0 100.0 99.4 AP009048.1:4154296-4153663 CRP is a global regulator that represses MdtEF multidrug efflux pump expression. fluoroquinolone, macrolide, penam
contig00046 16991 17866 CTX-M-15 0/0 100.0 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig00086 182 664 dfrA14 0/0 100.0 99.8 EU780012:2162-2645 dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli diaminopyrimidine
contig00010 80125 81297 emrA 0/0 100.0 99.9 AP009048:2810082-2811255 EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. fluoroquinolone
contig00010 81314 82852 emrB 0/0 100.0 99.8 U00096:2812615-2814154 emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. fluoroquinolone
contig00001 167043 168098 emrK 0/0 100.0 99.9 D78168:536-1592 emrK is a membrane fusion protein that is a homolog of EmrA. Together with the inner membrane transporter EmrY and the outer membrane channel TolC it mediates multidrug efflux. tetracycline
contig00010 79468 79998 emrR 0/0 100.0 100.0 U00096.3:2810769-2811300 EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. fluoroquinolone
contig00001 165505 167043 emrY 0/0 100.0 99.0 D78168:1591-3130 emrY is a multidrug transport that moves substrates across the inner membrane of the Gram-negative E. coli. It is a homolog of emrB. tetracycline
contig00048 7625 9268 eptA 0/0 100.0 100.0 AP009048:4340268-4338624 PmrC mediates the modification of Lipid A by the addition of 4-amino-4-deoxy-L-arabinose (L-Ara4N) and phosphoethanolamine resulting in a less negative cell membrane and decreased binding of polymyxin B. peptide
contig00008 38695 39888 Escherichia_coli_acrA 0/0 100.0 100.0 U00096.3:485619-484425 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. coli. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00034 38142 39275 Escherichia_coli_ampC 0/0 100.0 97.3 U00096.3:4378944-4377810 A class C ampC beta-lactamase (cephalosporinase) enzyme described in Escherichia coli shown clinically to confer resistance to penicillin-like and cephalosporin-class antibiotics. cephalosporin, penam
contig00001 231621 232925 Escherichia_coli_ampC1_beta-lactamase 0/0 100.0 99.9 FN649414.1:2765050-2766355 An ampC-like beta-lactamase identified from Escherichia coli. cephalosporin, penam
contig00006 894 2051 Escherichia_coli_ampH 0/0 100.0 98.8 AP012030.1:396711-395553 AmpH is a class C ampC-like beta-lactamase and penicillin-binding protein identified in Escherichia coli. cephalosporin, penam
contig00044 26094 27326 Escherichia_coli_mdfA 0/0 100.0 98.4 JQ394987:0-1233 Multidrug efflux pump in E. coli. This multidrug efflux system was originally identified as the Cmr/CmlA chloramphenicol exporter. benzalkonium_chloride, rhodamine, tetracycline
contig00001 168622 169236 evgA 0/0 100.0 100.0 BA000007.3:3212025-3212640 EvgA when phosphorylated is a positive regulator for efflux protein complexes emrKY and mdtEF. While usually phosphorylated in a EvgS dependent manner it can be phosphorylated in the absence of EvgS when overexpressed. fluoroquinolone, macrolide, penam, tetracycline
contig00001 169241 172834 evgS 0/0 100.0 99.7 U00096:2484373-2487967 EvgS is a sensor protein that phosphorylates the regulatory protein EvgA. evgS corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. fluoroquinolone, macrolide, penam, tetracycline
contig00007 97645 98373 gadW 0/0 100.0 94.7 CP015085.1:2552440-2551711 GadW is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. GadW inhibits GadX-dependent activation. GadW clearly represses gadX and in situations where GadX is missing activates gadA and gadBC. fluoroquinolone, macrolide, penam
contig00007 96453 97277 gadX 0/0 100.0 100.0 AP009048.1:3974604-3975429 GadX is an AraC-family regulator that promotes mdtEF expression to confer multidrug resistance. fluoroquinolone, macrolide, penam
contig00004 161513 161926 H-NS 0/0 100.0 99.5 BA000007.3:1738104-1737690 H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. cephalosporin, cephamycin, fluoroquinolone, macrolide, penam, tetracycline
contig00012 8068 8745 kdpE 0/0 100.0 100.0 U00096.3:721733-721055 kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. aminoglycoside
contig00015 88557 88940 marA 0/0 100.0 99.7 AP009048.1:1621287-1621671 In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00002 146181 147428 mdtA 0/0 100.0 99.5 U00096:2154015-2155263 MdtA is the membrane fusion protein of the multidrug efflux complex mdtABC. aminocoumarin
contig00002 143059 146181 mdtB 0/0 100.0 98.7 U00096:2155262-2158385 MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. aminocoumarin
contig00002 139981 143058 mdtC 0/0 100.0 99.8 U00096:2158385-2161463 MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. aminocoumarin
contig00007 101874 103031 mdtE 0/0 100.0 100.0 AP009048.1:3981183-3980025 MdtE is the membrane fusion protein of the MdtEF multidrug efflux complex. It shares 70% sequence similarity with AcrA. fluoroquinolone, macrolide, penam
contig00007 98736 101849 mdtF 0/0 100.0 100.0 U00096:3660413-3663527 MdtF is the multidrug inner membrane transporter for the MdtEF-TolC efflux complex. fluoroquinolone, macrolide, penam
contig00005 163790 165016 mdtG 0/0 100.0 99.4 CP000800.1:1192954-1191727 The MdtG protein also named YceE appears to be a member of the major facilitator superfamily of transporters and it has been reported when overexpressed to increase fosfomycin and deoxycholate resistances. mdtG is a member of the marA-soxS-rob regulon. fosfomycin
contig00004 8504 9712 mdtH 0/0 100.0 99.8 U00096:1125326-1124117 Multidrug resistance protein MdtH fluoroquinolone
contig00050 473 1684 mdtM 0/0 98.3 95.6 U00096.3:4568519-4567286 Multidrug resistance protein MdtM acridine_dye, fluoroquinolone, lincosamide, nucleoside, phenicol
contig00016 6677 7708 mdtN 0/0 100.0 100.0 AP009048.1:4307588-4306556 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride. acridine_dye, nucleoside
contig00016 7708 9759 mdtO 0/0 100.0 100.0 AP009048.1:4306557-4304505 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride acridine_dye, nucleoside
contig00016 9756 11222 mdtP 0/0 100.0 100.0 AP009048.1:4304509-4303042 Multidrug resistance efflux pump. Could be involved in resistance to puromycin acriflavine and tetraphenylarsonium chloride acridine_dye, nucleoside
contig00001 287883 288357 mphB 0/0 99.6 97.3 AE005174.2:3397370-3397847 The mphB gene encodes for MPH(2’)-II. This enzymes phosphorylates 14-membered and 16-membered macrolides. It phosphorylates macrolides in GTP- dependent manner at 2’-OH hydroxyl of desosamine sugar of macrolides. macrolide
contig00005 17130 18878 msbA 0/0 100.0 100.0 U00096.3:966620-968369 MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. nitroimidazole
contig00001 62154 63122 pmrF 0/0 100.0 100.0 U00096:2367070-2368039 PmrF is required for the synthesis and transfer of 4-amino-4-deoxy-L-arabinose (Ara4N) to Lipid A which allows gram-negative bacteria to resist the antimicrobial activity of cationic antimicrobial peptides and antibiotics such as polymyxin. pmrF corresponds to 1 locus in Pseudomonas aeruginosa PAO1 and 1 locus in Pseudomonas aeruginosa LESB58. peptide
contig00046 11694 12350 QnrS1 0/0 100.0 100.0 DQ485529.1:0-657 QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri fluoroquinolone
contig00046 23969 24784 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00046 20688 21548 TEM-1 0/0 100.0 99.9 AL513383:161910-162771 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. cephalosporin, monobactam, penam, penem
contig00072 2413 3659 tet(A) 0/0 97.8 100.0 AF534183.1:2970-4245 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. tetracycline
contig00043 5937 7424 tolC 0/0 100.0 99.7 FJ768952:0-1488 TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. aminocoumarin, aminoglycoside, carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, macrolide, penam, penem, peptide, phenicol, rifamycin, tetracycline, triclosan
contig00001 2055 3698 yojI 0/0 100.0 100.0 U00096.3:2308615-2306971 YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. peptide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00046 23105 23908 (AGly)strA 0/0 100 99.9 AB366441:22458-23261 (AGly)strA NA
contig00046 22269 23105 (AGly)strB 0/0 100 100.0 FJ474091:264-1100 (AGly)strB NA
contig00001 231621 232925 (Bla)AmpC1_Ecoli 0/0 100 99.9 FN649414:2765051-2766355 (Bla)AmpC1_Ecoli NA
contig00034 38142 39275 (Bla)AmpC2_Ecoli 0/0 100 97.3 CP002970:332756-333889 (Bla)AmpC2_Ecoli NA
contig00006 894 2051 (Bla)ampH_Ecoli 0/0 100 98.8 AP012030:395554-396711 (Bla)ampH_Ecoli NA
contig00046 16991 17866 (Bla)blaCTX-M-15 0/0 100 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig00046 20688 21548 (Bla)blaTEM-105 0/0 100 99.9 AF516720:215-1075 (Bla)blaTEM-105 NA
contig00012 60449 62350 (Bla)Penicillin_Binding_Protein_Ecoli 0/0 100 100.0 CP002291:664439-666340 (Bla)Penicillin_Binding_Protein_Ecoli NA
contig00046 11694 12350 (Flq)qnr-S1 0/0 100 100.0 AB187515:9737-10393 (Flq)qnr-S1 NA
contig00046 23969 24784 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00072 2385 3659 (Tet)tetA 0/0 100 100.0 JX424423:94438-95712 (Tet)tetA NA
contig00072 3690 4340 (Tet)tetR 0/0 100 100.0 HF545434:53576-54226 (Tet)tetR NA
contig00086 182 655 (Tmt)dfrA14 0/0 100 100.0 GU726917:72-545 (Tmt)dfrA14 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00046 23105 23932 aph(3’’)-Ib 0/0 100 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00046 22269 23105 aph(6)-Id 0/0 100 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00046 16991 17866 blaCTX-M-15 0/0 100 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00034 38142 39275 blaEC-15 0/0 100 98.6 NG_049081.1 class C extended-spectrum beta-lactamase EC-15 CEPHALOSPORIN
contig00046 20688 21548 blaTEM-1 0/0 100 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00086 182 655 dfrA14 0/0 100 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00046 11694 12350 qnrS1 0/0 100 100.0 NG_050543.1 quinolone resistance pentapeptide repeat protein QnrS1 QUINOLONE
contig00046 23969 24784 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00072 2385 3584 tet(A) 0/0 100 100.0 NG_048154.1 tetracycline efflux MFS transporter Tet(A) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 38695 39888 ACRA 0/0 100.0 100.0 MEG_399 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRA NA
contig00008 39911 43060 ACRB 0/0 100.0 100.0 MEG_401 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB NA
contig00001 264252 267365 ACRD 0/0 100.0 100.0 MEG_407 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ACRD NA
contig00033 8847 10004 ACRE 0/0 100.0 100.0 MEG_408 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRE NA
contig00033 5731 8835 ACRF 0/0 100.0 99.5 MEG_409 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRF NA
contig00033 10403 11065 ACRS 0/0 100.0 100.0 MEG_415 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ACRS NA
contig00006 894 2051 AMPH 0/0 100.0 98.8 MEG_729 Drugs:betalactams:Penicillin_binding_protein:AMPH NA
contig00046 23105 23932 APH3-DPRIME 0/0 100.0 100.0 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00046 22269 23105 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00002 159831 161683 ASMA 0/0 100.0 98.1 MEG_1180 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:ASMA NA
contig00043 29802 30623 BACA 0/0 100.0 100.0 MEG_1190 Drugs:Bacitracin:Undecaprenyl_pyrophosphate_phosphatase:BACA NA
contig00002 136446 137168 BAER 0/0 100.0 100.0 MEG_1192 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAER NA
contig00002 137165 138568 BAES 0/0 100.0 100.0 MEG_1193 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_regulator:BAES NA
contig00002 23573 24763 BCR 0/0 100.0 100.0 MEG_1210 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:BCR NA
contig00034 38142 39275 BLAEC 0/0 100.0 98.6 MEG_1282 Drugs:betalactams:Class_C_betalactamases:BLAEC NA
contig00037 2034 2732 CPXAR 0/0 100.0 100.0 MEG_2122 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR NA
contig00037 2729 4102 CPXAR 0/0 100.0 100.0 MEG_2121 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CPXAR NA
contig00045 15323 15955 CRP 0/0 100.0 99.4 MEG_2132 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:CRP NA
contig00086 182 655 DFRA 0/0 100.0 99.8 MEG_2517 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00010 80125 81297 EMRA 0/0 100.0 99.9 MEG_2722 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRA NA
contig00010 81314 82852 EMRB 0/0 100.0 99.8 MEG_2725 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRB NA
contig00056 16852 18042 EMRD 0/0 100.0 100.0 MEG_2729 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRD NA
contig00001 167043 168206 EMRK 0/0 100.0 99.9 MEG_2732 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRK NA
contig00010 79468 79998 EMRR 0/0 100.0 100.0 MEG_2734 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EMRR NA
contig00001 165505 167043 EMRY 0/0 100.0 99.1 MEG_2736 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:EMRY NA
contig00048 7625 9268 EPTA 0/0 100.0 100.0 MEG_2739 Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:EPTA NA
contig00001 169241 172834 EVGS 0/0 100.0 99.7 MEG_2870 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_regulator:EVGS NA
contig00007 97645 98373 GADW 0/0 100.0 100.0 MEG_3081 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADW NA
contig00007 96453 97277 GADX 0/0 100.0 100.0 MEG_3083 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:GADX NA
contig00004 161513 161926 HNS 0/0 100.0 99.5 MEG_3271 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_pumps:HNS NA
contig00012 8068 8745 KDPE 0/0 100.0 100.0 MEG_3448 Drugs:Aminoglycosides:Aminoglycoside_efflux_pumps:KDPE NA
contig00015 88551 88940 MARA 0/0 100.0 99.7 MEG_3662 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARA NA
contig00015 88102 88536 MARR 0/0 100.0 98.4 MEG_3663 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MARR NA
contig00044 26094 27326 MDFA 0/0 100.0 100.0 MEG_3737 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDFA NA
contig00002 146181 147428 MDTA 0/0 100.0 99.5 MEG_3746 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTA NA
contig00002 143059 146181 MDTB 0/0 100.0 98.7 MEG_3747 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTB NA
contig00002 139981 143058 MDTC 0/0 100.0 99.8 MEG_3749 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:MDTC NA
contig00007 101874 103031 MDTE 0/0 100.0 100.0 MEG_3751 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTE NA
contig00007 98736 101849 MDTF 0/0 100.0 100.0 MEG_3752 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTF NA
contig00005 163790 165016 MDTG 0/0 100.0 100.0 MEG_3753 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTG NA
contig00004 8504 9712 MDTH 0/0 100.0 99.8 MEG_3755 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTH NA
contig00003 220698 221027 MDTI 0/0 100.0 100.0 MEG_3756 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTI NA
contig00003 220346 220711 MDTJ 0/0 100.0 99.5 MEG_3757 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:MDTJ NA
contig00003 148945 150318 MDTK 0/0 100.0 99.9 MEG_3759 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:MDTK NA
contig00050 473 1684 MDTM 0/0 98.3 95.6 MEG_3761 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:MDTM NA
contig00016 6677 7708 MDTN 0/0 100.0 100.0 MEG_3763 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTN NA
contig00016 7708 9759 MDTO 0/0 100.0 100.0 MEG_3764 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTO NA
contig00016 9756 11222 MDTP 0/0 100.0 100.0 MEG_3765 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MDTP NA
contig00001 287883 288357 MPHB 0/0 99.6 97.3 MEG_4033 Drugs:MLS:Macrolide_phosphotransferases:MPHB NA
contig00005 17130 18878 MSBA 0/0 100.0 100.0 MEG_4061 Drugs:Multi-drug_resistance:Multi-drug_ABC_efflux_pumps:MSBA NA
contig00012 60449 62350 PBP2 0/0 100.0 100.0 MEG_5400 Drugs:betalactams:Penicillin_binding_protein:PBP2 NA
contig00001 231621 232925 PBP4B 0/0 100.0 99.9 MEG_5409 Drugs:betalactams:Penicillin_binding_protein:PBP4B NA
contig00001 62154 63122 PMRF 0/0 100.0 100.0 MEG_5801 Drugs:Cationic_antimicrobial_peptides:Lipid_A_modification:PMRF NA
contig00046 11694 12350 QNRS 0/0 100.0 100.0 MEG_6020 Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS NA
contig00027 21726 22595 ROBA 0/0 100.0 98.8 MEG_6082 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_RND_efflux_pumps:ROBA NA
contig00016 33290 33612 SOXS 0/0 99.7 99.7 MEG_6551 Multi-compound:Drug_and_biocide_and_metal_resistance:Drug_and_biocide_and_metal_resistance_regulator:SOXS NA
contig00046 23969 24784 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00046 20321 21566 TEM 0/0 98.3 99.4 MEG_6875 Drugs:betalactams:Class_A_betalactamases:TEM NA
contig00072 2385 3659 TETA 0/0 100.0 100.0 MEG_7024 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA NA
contig00001 2055 3698 YOGI 0/0 100.0 100.0 MEG_7842 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_ABC_efflux_pumps:YOGI NA
ID089
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00080 8052 8912 aac(3)-IId_1 0/0 100.0 99.9 EU022314 aac(3)-IId Gentamicin, Tobramycin
contig00080 6639 7441 aph(3’’)-Ib_2 0/0 99.9 100.0 AF024602 aph(3’’)-Ib Streptomycin
contig00080 5803 6639 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00114 93 905 blaNDM-1_1 0/0 100.0 100.0 FN396876 blaNDM-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00003 199899 200729 blaOXA-356_1 0/0 100.0 100.0 KF297585 blaOXA-356
contig00094 129 971 blaOXA-420_1 0/0 100.0 100.0 AB983359 blaOXA-420
contig00092 121 1005 mph(E)_1 0/0 100.0 100.0 DQ839391 mph(E) Erythromycin
contig00092 1061 2536 msr(E)_1 0/0 100.0 100.0 FR751518 msr(E)
contig00080 2375 3190 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00094 2244 3365 tet(39)_1 0/0 100.0 99.9 KT346360 tet(39) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00080 8052 8912 AAC(3)-IId 0/0 100.0 99.9 EU022314.1:0-861 AAC(3)-IId is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig00080 6639 7442 APH(3’’)-Ib 0/0 100.0 99.9 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00080 5803 6639 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00114 909 1243 determinant_of_bleomycin_resistance 0/0 91.5 100.0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide
contig00092 121 1005 mphE 0/0 100.0 100.0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 macrolide
contig00092 1061 2536 msrE 0/0 100.0 100.0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00114 93 905 NDM-1 0/0 100.0 100.0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. carbapenem, cephalosporin, cephamycin, penam
contig00003 199899 200729 OXA-356 0/0 100.0 100.0 KF297585:0-831 OXA-356 is a beta-lactamase. From the Lahey list of OXA beta-lactamases. cephalosporin, penam
contig00094 129 971 OXA-420 0/0 100.0 100.0 AB983359:2425-3268 From the Lahey list of beta-lactamases. Not yet released. cephalosporin, penam
contig00080 2375 3190 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00094 2178 3365 tet(39) 0/0 100.0 99.9 AY743590:0-1188 Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00080 8052 8912 (AGly)aac3-IId 0/0 100 99.9 EU022314:1-861 (AGly)aac3-IId NA
contig00080 6639 7442 (AGly)strA 0/0 100 100.0 AB366441:22458-23261 (AGly)strA NA
contig00080 5803 6639 (AGly)strB 0/0 100 100.0 FJ474091:264-1100 (AGly)strB NA
contig00114 93 905 (Bla)blaNDM-1 0/0 100 100.0 JQ080305:1-813 (Bla)blaNDM-1 NA
contig00003 199899 200729 (Bla)blaOXA-230 0/0 100 99.0 JQ422054:101-931 (Bla)blaOXA-230 NA
contig00094 129 971 (Bla)blaOXA-58 0/0 100 99.6 AY665723:3301-4143 (Bla)blaOXA-58 NA
contig00092 121 1005 (MLS)mph(E) 0/0 100 99.9 JF769133:8777-9661 (MLS)mph(E) NA
contig00092 1061 2536 (MLS)msr(E) 0/0 100 100.0 JF769133:7246-8721 (MLS)msr(E) NA
contig00080 2375 3190 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00094 2178 3365 (Tet)tet(39) 0/0 100 99.9 AY743590:749-1936 (Tet)tet(39) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00080 8052 8912 aac(3)-IId 0/0 100.0 100.0 NG_047251.1 aminoglycoside N-acetyltransferase AAC(3)-IId GENTAMICIN
contig00080 6639 7466 aph(3’’)-Ib 0/0 100.0 99.9 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00080 5803 6639 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00114 93 905 blaNDM-1 0/0 100.0 100.0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1 CARBAPENEM
contig00003 199899 200729 blaOXA-356 0/0 100.0 100.0 NG_049649.1 OXA-229 family carbapenem-hydrolyzing class D beta-lactamase OXA-356 CARBAPENEM
contig00094 129 971 blaOXA-420 0/0 100.0 100.0 NG_049708.1 OXA-58 family carbapenem-hydrolyzing class D beta-lactamase OXA-420 CARBAPENEM
contig00114 909 1243 ble-MBL 0/0 91.5 100.0 NG_047559.1 bleomycin binding protein Ble-MBL BLEOMYCIN
contig00092 121 1005 mph(E) 0/0 100.0 100.0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase MACROLIDE
contig00092 1061 2536 msr(E) 0/0 100.0 100.0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E) MACROLIDE
contig00080 2375 3190 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00094 2178 3365 tet(39) 0/0 100.0 99.9 NG_048137.1 tetracycline efflux MFS transporter Tet(39) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00080 8052 8912 AAC3 0/0 100.0 100.0 MEG_64 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 NA
contig00080 6639 7466 APH3-DPRIME 0/0 100.0 99.9 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00080 5803 6639 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00114 909 1243 BRP 0/0 91.5 100.0 MEG_1477 Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP NA
contig00092 121 1005 MPHE 0/0 100.0 100.0 MEG_4044 Drugs:MLS:Macrolide_phosphotransferases:MPHE NA
contig00092 1061 2536 MSRE 0/0 100.0 100.0 MEG_4075 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE NA
contig00114 93 905 NDM 0/0 100.0 100.0 MEG_4143 Drugs:betalactams:Class_B_betalactamases:NDM NA
contig00003 199864 200829 OXA 0/0 100.0 98.9 MEG_5220 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00094 123 998 OXA 0/0 96.2 99.5 MEG_5259 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00080 2375 3190 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00094 2178 3365 TET39 0/0 100.0 99.9 MEG_6987 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 NA
ID186
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00035 4721 5254 ant(2’’)-Ia_13 0/0 100 99.1 DQ176450 ant(2’’)-Ia Gentamicin, Tobramycin
contig00024 9 1160 blaADC-25_1 0/0 100 99.7 EF016355 blaADC-25
contig00006 209827 210651 blaOXA-69_1 0/0 100 100.0 AY859527 blaOXA-69 Amoxicillin, Ampicillin
contig00036 448 1263 sul2_2 0/0 100 100.0 AY034138 sul2 Sulfamethoxazole
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00004 12051 13397 abeM 0/0 100 98.9 AB204810:186-1533 AbeM is an multidrug efflux pump found in Acinetobacter baumannii. acridine_dye, fluoroquinolone, triclosan
contig00003 77408 77737 abeS 0/0 100 100.0 CP001172.1:1249348-1249018 AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. aminocoumarin, macrolide
contig00025 28121 29410 Acinetobacter_baumannii_AbaF 0/0 100 97.9 CP000521.1:1558523-1557233 Expression of abaF in E. coli resulted in increased resistance to fosfomycin. fosfomycin
contig00010 117010 118314 Acinetobacter_baumannii_AbaQ 0/0 100 100.0 CP001182.2:2256889-2255584 AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii fluoroquinolone
contig00008 90140 91618 Acinetobacter_baumannii_AmvA 0/0 100 100.0 FJ911554.1:176-1655 AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. acridine_dye, macrolide
contig00024 9 1160 ADC-73 0/0 100 99.9 KP881233.1:0-1152 A class C ADC beta-lactamase and cephalosporinase found in Acinetobacter baumannii cephalosporin
contig00014 12728 13918 adeA 0/0 100 97.7 AF370885.1:3438-4629 AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. glycylcycline, tetracycline
contig00014 9621 12728 adeB 0/0 100 97.8 AF370885.1:4628-7736 AdeB is the multidrug transporter of the adeABC efflux system. glycylcycline, tetracycline
contig00014 8147 9544 adeC 0/0 100 95.4 CP013924.1:2063742-2065140 AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. glycylcycline, tetracycline
contig00003 68464 71643 adeF 0/0 100 100.0 CT025801.2:0-3180 AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. fluoroquinolone, tetracycline
contig00003 71650 72870 adeG 0/0 100 100.0 CT025800.2:0-1221 AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00003 67003 68454 adeH 0/0 100 100.0 CT025802.2:0-1452 AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00013 41683 42933 adeI 0/0 100 100.0 CP001182.2:3283426-3284677 AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00013 42946 46122 adeJ 0/0 100 99.6 AY769962:2434-5611 AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00013 46122 47576 adeK 0/0 100 98.7 AY769962:5610-7065 AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00003 73086 74099 adeL 0/0 100 99.4 KR297239.1:1428-414 AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. fluoroquinolone, tetracycline
contig00008 35419 36072 adeN 0/0 100 98.0 KF147862:0-654 AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00014 14064 14807 adeR 0/0 100 100.0 HM440348:0-744 AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. glycylcycline, tetracycline
contig00014 14839 15924 adeS 0/0 100 99.7 HM440348:775-1861 AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. glycylcycline, tetracycline
contig00035 4721 5254 ANT(2’’)-Ia 0/0 100 98.9 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00006 209827 210651 OXA-69 0/0 100 100.0 CU459141.1:2175316-2176141 OXA-69 is a beta-lactamase found in A. baumannii cephalosporin, penam
contig00036 448 1263 sul2 0/0 100 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00035 4721 5254 (AGly)aadB 0/0 100 98.9 JQ690540:4275-4808 (AGly)aadB NA
contig00021 23718 24506 (AGly)ant(3’’)-IIa 0/0 100 98.9 NG_054648:101-889 (AGly)ant(3’’)-IIa NA
contig00010 129920 130939 (Bla)BlaA1 0/0 100 100.0 NC_010410:1803480-1804499 (Bla)BlaA1 NA
contig00019 57121 58395 (Bla)BlaA2 0/0 100 100.0 NC_010410:2507740-2509014 (Bla)BlaA2 NA
contig00024 9 1160 (Bla)blaADC-73 0/0 100 99.9 KP881233:1-1152 (Bla)blaADC-73 NA
contig00006 209827 210651 (Bla)blaOXA-69 0/0 100 100.0 AY750911:1-825 (Bla)blaOXA-69 NA
contig00006 30952 31647 (Bla)Mbl 0/0 100 100.0 NC_010410:c1997136-1996441 (Bla)Mbl NA
contig00002 274643 275605 (Bla)Zn-dependent_hydrolase 0/0 100 100.0 NC_010410:882015-882977 (Bla)Zn-dependent_hydrolase NA
contig00036 448 1263 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00035 4721 5254 ant(2’’)-Ia 0/0 100 99.1 NG_052432.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00021 23718 24506 ant(3’’)-IIa 0/0 100 100.0 NG_054646.1 aminoglycoside nucleotidyltransferase ANT(3’’)-IIa SPECTINOMYCIN, STREPTOMYCIN
contig00024 9 1160 blaADC-73 0/0 100 99.9 NG_048678.1 class C extended-spectrum beta-lactamase ADC-73 CEPHALOSPORIN
contig00006 209827 210651 blaOXA-69 0/0 100 100.0 NG_049809.1 OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 CARBAPENEM
contig00036 448 1263 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00025 28121 29410 ABAF 0/0 100.0 97.9 MEG_369 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF NA
contig00010 117010 118314 ABAQ 0/0 100.0 100.0 MEG_370 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ NA
contig00004 12051 13397 ABEM 0/0 100.0 98.9 MEG_372 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM NA
contig00003 77408 77737 ABES 0/0 100.0 100.0 MEG_379 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES NA
contig00024 9 1160 ADC 0/0 100.0 99.9 MEG_666 Drugs:betalactams:Class_C_betalactamases:ADC NA
contig00014 12728 13918 ADEA 0/0 100.0 97.7 MEG_677 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA NA
contig00014 9621 12728 ADEB 0/0 100.0 97.8 MEG_678 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB NA
contig00014 8147 9544 ADEC 0/0 100.0 95.4 MEG_679 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC NA
contig00003 71650 72870 ADEF 0/0 100.0 100.0 MEG_683 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF NA
contig00003 68464 71643 ADEG 0/0 100.0 100.0 MEG_684 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG NA
contig00003 67003 68454 ADEH 0/0 100.0 100.0 MEG_685 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH NA
contig00013 41683 42933 ADEI 0/0 100.0 100.0 MEG_686 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI NA
contig00013 42946 46122 ADEJ 0/0 100.0 99.6 MEG_692 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ NA
contig00013 46122 47576 ADEK 0/0 100.0 99.0 MEG_696 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK NA
contig00003 73086 74099 ADEL 0/0 100.0 99.5 MEG_699 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL NA
contig00008 35419 36072 ADEN 0/0 100.0 100.0 MEG_701 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN NA
contig00014 14064 14807 ADER 0/0 100.0 100.0 MEG_703 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER NA
contig00014 14839 15924 ADES 0/0 100.0 99.7 MEG_704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES NA
contig00001 406388 407104 ADET2 0/0 100.0 98.9 MEG_706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 NA
contig00008 90140 91618 AMVA 0/0 100.0 100.0 MEG_733 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA NA
contig00021 23718 24506 ANT3-DPRIME 0/0 100.0 100.0 MEG_913 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00010 129920 130939 BLAA 0/0 100.0 100.0 MEG_1246 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00019 57121 58395 BLAA 0/0 100.0 100.0 MEG_1247 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00005 71704 72693 MEXT 0/0 100.0 98.8 MEG_3934 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT NA
contig00006 209782 210733 OXA 3/3 98.9 97.5 MEG_5236 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00036 448 1263 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
ID259
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00154 3439 4240 aadA2_1 0/0 97.9 99.9 NC_010870 aadA2 Streptomycin
contig00146 1510 2312 aph(3’’)-Ib_2 0/0 99.9 100.0 AF024602 aph(3’’)-Ib Streptomycin
contig00146 674 1510 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00040 19695 20840 blaACT-6_1 0/0 100.0 91.0 FJ237366 blaACT-6
contig00099 5508 6383 blaCTX-M-3_1 0/0 100.0 100.0 Y10278 blaCTX-M-3 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00099 3866 4726 blaTEM-1B_1 0/0 100.0 100.0 AY458016 blaTEM-1B Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00154 4638 5135 dfrA12_8 0/0 100.0 100.0 AM040708 dfrA12 Trimethoprim
contig00058 20141 20566 fosA_1 0/0 100.0 95.1 M85195 fosA Fosfomycin
contig00099 13087 13743 qnrS1_1 0/0 100.0 100.0 AB187515 qnrS1 Ciprofloxacin
contig00154 2095 2961 sul1_5 0/0 100.0 99.9 EU780013 sul1 Sulfamethoxazole
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00154 3439 4218 aadA2 0/0 100.0 99.9 AF156486:5012-5792 aadA2 is an aminoglycoside nucleotidyltransferase gene encoded by plasmids and integrons in K. pneumoniae Salmonella spp. Corynebacterium glutamicum C. freundii and Aeromonas spp. aminoglycoside
contig00040 19695 20840 ACT-6 0/0 100.0 91.0 FJ237366:40-1186 ACT-6 is a beta-lactamase found in Klebsiella pneumoniae carbapenem, cephalosporin, cephamycin, penam
contig00146 1510 2313 APH(3’’)-Ib 0/0 100.0 99.9 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00146 674 1510 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00099 5508 6383 CTX-M-3 0/0 100.0 100.0 Y10278:0-876 CTX-M-3 is a beta-lactamase found in Citrobacter freundii cephalosporin
contig00154 4638 5135 dfrA12 0/0 100.0 100.0 GU585907.1:22103-21605 dfrA12 is an integron-encoded dihydrofolate reductase found in Vibrio cholerae diaminopyrimidine
contig00074 14977 16170 Enterobacter_cloacae_acrA 0/0 100.0 95.2 DQ679966:299-1493 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00058 20141 20566 FosA2 2/4 99.5 92.3 EU487198:216-642 An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. fosfomycin
contig00099 13087 13743 QnrS1 0/0 100.0 100.0 DQ485529.1:0-657 QnrS1 is a plasmid-mediated quinolone resistance protein found in Shigella flexneri fluoroquinolone
contig00139 4345 4708 ramA 0/0 97.1 90.9 JQ727668:0-375 RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00154 2095 2934 sul1 0/0 100.0 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00099 3866 4726 TEM-1 0/0 100.0 99.9 AL513383:161910-162771 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. cephalosporin, monobactam, penam, penem
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00154 3439 4218 (AGly)aadA2 0/0 100.0 99.9 X68227:66-945 (AGly)aadA2 NA
contig00146 1510 2313 (AGly)strA 0/0 100.0 100.0 AB366441:22458-23261 (AGly)strA NA
contig00146 674 1510 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00040 19695 20840 (Bla)blaACT-6 0/0 100.0 91.0 FJ237366:41-1186 (Bla)blaACT-6 NA
contig00099 5508 6383 (Bla)blaCTX-M-3 0/0 100.0 100.0 Y10278:1-876 (Bla)blaCTX-M-3 NA
contig00099 3866 4726 (Bla)blaTEM-105 0/0 100.0 99.9 AF516720:215-1075 (Bla)blaTEM-105 NA
contig00058 20141 20566 (Fcyn)FosA2 2/4 99.5 92.3 EU487198:217-642 (Fcyn)FosA2 NA
contig00099 13087 13743 (Flq)qnr-S1 0/0 100.0 100.0 AB187515:9737-10393 (Flq)qnr-S1 NA
contig00154 2095 2934 (Sul)sul1 0/0 100.0 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig00154 4638 5135 (Tmt)dfrA12 0/0 100.0 100.0 Z21672:310-807 (Tmt)dfrA12 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00154 3439 4230 aadA2 0/0 100 100.0 NG_047343.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA2 STREPTOMYCIN
contig00146 1510 2337 aph(3’’)-Ib 0/0 100 99.9 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00146 674 1510 aph(6)-Id 0/0 100 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00040 19695 20840 blaACT-53 0/0 100 100.0 NG_055522.1 cephalosporin-hydrolyzing class C beta-lactamase ACT-53 CEPHALOSPORIN
contig00099 5508 6383 blaCTX-M-3 0/0 100 100.0 NG_048979.1 class A extended-spectrum beta-lactamase CTX-M-3 CEPHALOSPORIN
contig00099 3866 4726 blaTEM-1 0/0 100 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00154 4638 5135 dfrA12 0/0 100 100.0 NG_047689.1 trimethoprim-resistant dihydrofolate reductase DfrA12 TRIMETHOPRIM
contig00058 20141 20566 fosA 0/0 100 95.1 NG_050405.1 fosfomycin resistance glutathione transferase FosA FOSFOMYCIN
contig00099 13087 13743 qnrS1 0/0 100 100.0 NG_050543.1 quinolone resistance pentapeptide repeat protein QnrS1 QUINOLONE
contig00154 2095 2934 sul1 0/0 100 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00074 14977 16170 ACRB 0/0 100.0 95.2 MEG_402 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB NA
contig00040 19695 20840 ACT 0/0 100.0 100.0 MEG_441 Drugs:betalactams:Class_C_betalactamases:ACT NA
contig00154 3439 4240 ANT3-DPRIME 0/0 97.9 99.9 MEG_975 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00146 1510 2337 APH3-DPRIME 0/0 100.0 99.9 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00146 674 1510 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00099 5137 6622 CTX 0/0 100.0 99.8 MEG_2421 Drugs:betalactams:Class_A_betalactamases:CTX NA
contig00154 4638 5135 DFRA 0/0 100.0 100.0 MEG_2551 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00058 19987 20566 FOSA 2/4 99.3 92.8 MEG_2990 Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA NA
contig00099 13087 13743 QNRS 0/0 100.0 100.0 MEG_6020 Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRS NA
contig00139 4345 4708 RAMA 0/0 97.1 90.9 MEG_6044 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA NA
contig00154 1968 2935 SULI 0/0 100.0 100.0 MEG_6615 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI NA
contig00099 3499 4744 TEM 0/0 98.3 99.4 MEG_6875 Drugs:betalactams:Class_A_betalactamases:TEM NA
ORTHO015E
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00032 34599 35750 blaADC-25_1 0/0 100.0 97.1 EF016355 blaADC-25
contig00061 92 904 blaNDM-1_1 0/0 100.0 100.0 FN396876 blaNDM-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Cefixime, Cefotaxime, Cefoxitin, Ceftazidime, Ertapenem, Imipenem, Meropenem, Piperacillin, Piperacillin+Tazobactam
contig00018 70816 71640 blaOXA-98_1 0/0 100.0 99.9 EU255288 blaOXA-98
contig00033 19356 20569 floR_2 0/0 99.9 98.3 AF118107 floR Chloramphenicol, Florfenicol
contig00033 29463 30347 mph(E)_1 0/0 100.0 100.0 DQ839391 mph(E) Erythromycin
contig00033 27932 29407 msr(E)_1 0/0 100.0 100.0 FR751518 msr(E)
contig00014 89308 90123 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00033 22089 23210 tet(39)_1 0/0 100.0 100.0 KT346360 tet(39) Doxycycline, Tetracycline
contig00014 87488 88693 tet(B)_1 0/0 100.0 100.0 AP000342 tet(B) Doxycycline, Tetracycline, Minocycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00008 23968 25314 abeM 0/0 100.0 100.0 AB204810:186-1533 AbeM is an multidrug efflux pump found in Acinetobacter baumannii. acridine_dye, fluoroquinolone, triclosan
contig00002 42631 42960 abeS 0/0 100.0 97.9 CP001172.1:1249348-1249018 AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. aminocoumarin, macrolide
contig00005 10124 11413 Acinetobacter_baumannii_AbaF 0/0 100.0 96.8 CP000521.1:1558523-1557233 Expression of abaF in E. coli resulted in increased resistance to fosfomycin. fosfomycin
contig00006 91623 92927 Acinetobacter_baumannii_AbaQ 0/0 100.0 95.6 CP001182.2:2256889-2255584 AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii fluoroquinolone
contig00022 42414 43892 Acinetobacter_baumannii_AmvA 0/0 100.0 97.9 FJ911554.1:176-1655 AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. acridine_dye, macrolide
contig00032 34599 35750 ADC-2 0/0 100.0 99.7 AY177427.1:1141-2293 ADC-2 is a beta-lactamase found in Oligella urethralis. cephalosporin
contig00047 8886 10076 adeA 0/0 100.0 97.7 AF370885.1:3438-4629 AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. glycylcycline, tetracycline
contig00047 10076 13183 adeB 0/0 100.0 98.1 AF370885.1:4628-7736 AdeB is the multidrug transporter of the adeABC efflux system. glycylcycline, tetracycline
contig00002 33687 36866 adeF 0/0 100.0 97.7 CT025801.2:0-3180 AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. fluoroquinolone, tetracycline
contig00002 36873 38093 adeG 0/0 100.0 98.4 CT025800.2:0-1221 AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00002 32226 33677 adeH 0/0 100.0 98.5 CT025802.2:0-1452 AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00003 39967 41217 adeI 0/0 100.0 99.7 CP001182.2:3283426-3284677 AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00003 41230 44406 adeJ 0/0 100.0 99.6 AY769962:2434-5611 AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00003 44406 45860 adeK 0/0 100.0 98.8 AY769962:5610-7065 AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00002 38309 39322 adeL 0/0 100.0 99.7 KR297239.1:1428-414 AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. fluoroquinolone, tetracycline
contig00031 26224 26877 adeN 0/0 100.0 98.5 KF147862:0-654 AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00047 7997 8740 adeR 0/0 100.0 98.1 HM440348:0-744 AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. glycylcycline, tetracycline
contig00047 6901 7965 adeS 0/0 98.1 95.8 HM440348:775-1861 AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. glycylcycline, tetracycline
contig00061 908 1273 determinant_of_bleomycin_resistance 0/0 100.0 100.0 KC503911.1:9883-10249 A novel bleomycin resistance protein encoded by a metallo-beta-lactamase-associated ble gene. Expression of BRP(MBL) confers resistance to bleomycin and bleomycin-like antibiotics in Enterobacteriaceae and Acinetobacter where it is co-expressed with an MBL and controlled by the same promoter region. glycopeptide
contig00033 19356 20570 floR 0/0 100.0 99.9 AF231986:3307-4522 floR is a plasmid or chromosome-encoded chloramphenicol exporter that is found in Bordetella bronchiseptica Escherichia coli Klebsiella pneumoniae Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 and Vibrio cholerae phenicol
contig00033 29463 30347 mphE 0/0 100.0 100.0 DQ839391.1:13757-12872 mphE is a macrolide phosphotransferase and resistance gene identified on a plasmid pRSB105 macrolide
contig00033 27932 29407 msrE 0/0 100.0 100.0 EU294228.1:21241-22717 MsrE is an ABC-F subfamily protein expressed to Klebsiella pneumoniae that confers resistance to erythromycin and streptogramin B antibiotics. It is associated with plasmid DNA. It is also 100% identical to ABC-F type ribosomal protection protein Msr(E) which is in multiple species. lincosamide, macrolide, oxazolidinone, phenicol, pleuromutilin, streptogramin, tetracycline
contig00061 92 904 NDM-1 0/0 100.0 100.0 FN396876:3219-2406 NDM-1 is a metallo-beta-lactamase isolated from Klebsiella pneumoniae with nearly complete resistance to all beta-lactam antibiotics. carbapenem, cephalosporin, cephamycin, penam
contig00018 70816 71640 OXA-98 0/0 100.0 99.9 AM279652:0-825 OXA-98 is a beta-lactamase found in A. baumannii cephalosporin, penam
contig00014 89308 90123 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00033 22089 23276 tet(39) 0/0 100.0 100.0 AY743590:0-1188 Tet39 is a tetracycline efflux pump found in Gram-negative bacteria including Brevundimonas Stenotrophomonas Enterobacter Alcaligenes Acinetobacter and Providencia. tetracycline
contig00014 87488 88693 tet(B) 0/0 100.0 99.8 AB089595:0-1206 Tet(B) is a tetracycline efflux protein expressed in many Gram-negative bacteria. It confers resistance to tetracycline doxycycline and minocycline but not tigecycline. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00007 119028 119816 (AGly)ant(3’’)-IIa 0/0 100.0 100.0 NG_054648:101-889 (AGly)ant(3’’)-IIa NA
contig00006 104506 105523 (Bla)BlaA1 0/0 99.8 90.8 NC_010410:1803480-1804499 (Bla)BlaA1 NA
contig00020 19863 21131 (Bla)BlaA2 0/0 99.5 97.4 NC_010410:2507740-2509014 (Bla)BlaA2 NA
contig00032 34599 35750 (Bla)blaADC-2 0/0 100.0 99.7 NG_048644:101-1252 (Bla)blaADC-2 NA
contig00061 92 904 (Bla)blaNDM-1 0/0 100.0 100.0 JQ080305:1-813 (Bla)blaNDM-1 NA
contig00018 70816 71640 (Bla)blaOXA-98 0/0 100.0 99.9 AM279652:1-825 (Bla)blaOXA-98 NA
contig00021 33771 34466 (Bla)Mbl 0/0 100.0 98.0 NC_010410:c1997136-1996441 (Bla)Mbl NA
contig00019 50318 51280 (Bla)Zn-dependent_hydrolase 0/0 100.0 98.7 NC_010410:882015-882977 (Bla)Zn-dependent_hydrolase NA
contig00033 29463 30347 (MLS)mph(E) 0/0 100.0 99.9 JF769133:8777-9661 (MLS)mph(E) NA
contig00033 27932 29407 (MLS)msr(E) 0/0 100.0 100.0 JF769133:7246-8721 (MLS)msr(E) NA
contig00033 19356 20570 (Phe)floR 0/0 100.0 99.8 AKLJ01000508:383-1597 (Phe)floR NA
contig00014 89308 90123 (Sul)sul2 0/0 100.0 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00033 22089 23276 (Tet)tet(39) 0/0 100.0 100.0 AY743590:749-1936 (Tet)tet(39) NA
contig00014 87488 88693 (Tet)tetB 0/0 100.0 99.8 AB089594:1-1206 (Tet)tetB NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00007 119028 119816 ant(3’’)-IIa 0/0 100 100.0 NG_054648.1 aminoglycoside nucleotidyltransferase ANT(3’’)-IIa SPECTINOMYCIN, STREPTOMYCIN
contig00032 34599 35750 blaADC-158 0/0 100 100.0 NG_055786.1 class C beta-lactamase ADC-158 CEPHALOSPORIN
contig00061 92 904 blaNDM-1 0/0 100 100.0 NG_049326.1 subclass B1 metallo-beta-lactamase NDM-1 CARBAPENEM
contig00018 70816 71640 blaOXA-694 0/0 100 99.9 NG_062316.1 OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-694 BETA-LACTAM
contig00061 908 1273 ble-MBL 0/0 100 100.0 NG_047559.1 bleomycin binding protein Ble-MBL BLEOMYCIN
contig00033 19356 20570 floR 0/0 100 100.0 NG_047869.1 chloramphenicol/florfenicol efflux MFS transporter FloR CHLORAMPHENICOL, FLORFENICOL
contig00033 29463 30347 mph(E) 0/0 100 100.0 NG_064660.1 Mph(E) family macrolide 2’-phosphotransferase MACROLIDE
contig00033 27932 29407 msr(E) 0/0 100 100.0 NG_048007.1 ABC-F type ribosomal protection protein Msr(E) MACROLIDE
contig00014 89308 90123 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00033 22089 23276 tet(39) 0/0 100 100.0 NG_048137.1 tetracycline efflux MFS transporter Tet(39) TETRACYCLINE
contig00014 87488 88693 tet(B) 0/0 100 100.0 NG_048161.1 tetracycline efflux MFS transporter Tet(B) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00005 10124 11413 ABAF 0/0 100.0 96.8 MEG_369 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF NA
contig00006 91623 92927 ABAQ 0/0 100.0 95.6 MEG_370 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ NA
contig00008 23968 25314 ABEM 0/0 100.0 100.0 MEG_373 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM NA
contig00002 42631 42960 ABES 0/0 100.0 99.4 MEG_378 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES NA
contig00032 34599 35750 ADC 0/0 100.0 100.0 MEG_575 Drugs:betalactams:Class_C_betalactamases:ADC NA
contig00047 8886 10076 ADEA 0/0 100.0 97.7 MEG_677 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA NA
contig00047 10076 13183 ADEB 0/0 100.0 98.1 MEG_678 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB NA
contig00002 33687 36866 ADEG 0/0 100.0 97.7 MEG_684 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG NA
contig00002 32226 33677 ADEH 0/0 100.0 98.5 MEG_685 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH NA
contig00003 39967 41217 ADEI 0/0 100.0 99.9 MEG_689 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI NA
contig00003 41230 44406 ADEJ 0/0 100.0 99.6 MEG_692 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ NA
contig00003 44406 45860 ADEK 0/0 100.0 99.1 MEG_698 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK NA
contig00002 38309 39322 ADEL 0/0 100.0 99.7 MEG_700 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL NA
contig00031 26224 26877 ADEN 0/0 100.0 98.5 MEG_702 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN NA
contig00047 7997 8740 ADER 0/0 100.0 98.1 MEG_703 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER NA
contig00047 6901 7965 ADES 0/0 98.1 95.8 MEG_704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES NA
contig00047 5773 6687 ADET1 0/0 100.0 96.7 MEG_705 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET1 NA
contig00013 46951 47667 ADET2 0/0 100.0 98.9 MEG_706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 NA
contig00022 42414 43892 AMVA 0/0 100.0 97.9 MEG_733 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA NA
contig00007 119028 119816 ANT3-DPRIME 0/0 100.0 100.0 MEG_899 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00006 104506 105523 BLAA 0/0 99.8 90.8 MEG_1246 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00020 19863 21131 BLAA 0/0 99.5 97.4 MEG_1247 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00061 908 1273 BRP 0/0 100.0 100.0 MEG_1477 Drugs:Glycopeptides:Bleomycin_resistance_protein:BRP NA
contig00033 19356 20570 FLOR 0/0 100.0 100.0 MEG_2923 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR NA
contig00002 36873 38093 MEXE 1/3 100.0 99.1 MEG_3910 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:MEXE NA
contig00039 1751 2740 MEXT 0/0 100.0 98.7 MEG_3934 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT NA
contig00033 29463 30347 MPHE 0/0 100.0 100.0 MEG_4044 Drugs:MLS:Macrolide_phosphotransferases:MPHE NA
contig00033 27932 29407 MSRE 0/0 100.0 100.0 MEG_4075 Drugs:MLS:MLS_resistance_ABC_efflux_pumps:MSRE NA
contig00061 92 904 NDM 0/0 100.0 100.0 MEG_4143 Drugs:betalactams:Class_B_betalactamases:NDM NA
contig00018 70771 71722 OXA 3/3 99.0 98.5 MEG_5236 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00014 89308 90123 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00033 22089 23276 TET39 0/0 100.0 100.0 MEG_6987 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TET39 NA
contig00014 87488 88693 TETB 0/0 100.0 100.0 MEG_7042 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETB NA
ORTHO037E
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00037 4721 5254 ant(2’’)-Ia_13 0/0 100 99.1 DQ176450 ant(2’’)-Ia Gentamicin, Tobramycin
contig00002 9 1160 blaADC-25_1 0/0 100 99.8 EF016355 blaADC-25
contig00006 209855 210679 blaOXA-69_1 0/0 100 100.0 AY859527 blaOXA-69 Amoxicillin, Ampicillin
contig00038 448 1263 sul2_2 0/0 100 100.0 AY034138 sul2 Sulfamethoxazole
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00007 12051 13397 abeM 0/0 100 98.9 AB204810:186-1533 AbeM is an multidrug efflux pump found in Acinetobacter baumannii. acridine_dye, fluoroquinolone, triclosan
contig00009 77408 77737 abeS 0/0 100 100.0 CP001172.1:1249348-1249018 AbeS in an efflux pump of the SMR family of transporters found in Acinetobacter baumannii. aminocoumarin, macrolide
contig00004 134203 135492 Acinetobacter_baumannii_AbaF 0/0 100 97.9 CP000521.1:1558523-1557233 Expression of abaF in E. coli resulted in increased resistance to fosfomycin. fosfomycin
contig00011 116965 118269 Acinetobacter_baumannii_AbaQ 0/0 100 100.0 CP001182.2:2256889-2255584 AbaQ is an MFS transporter mainly involved in the extrusion of quinolone-type drugs in A. baumannii fluoroquinolone
contig00012 90155 91633 Acinetobacter_baumannii_AmvA 0/0 100 100.0 FJ911554.1:176-1655 AmvA has 14 alpha-helical transmembrane segments qualifying it as a member of the DHA2 transporter family of the major facilitator superfamily (MFS). When AmvA was expressed in E. coli the cells had at least four-fold decreased susceptibility to erythromycin acridine orange acriflavine deoxycholate and methyl viologen. AmvA from the AC0037 strain of A. baumannii was tested. acridine_dye, macrolide
contig00002 9 1160 ADC-73 0/0 100 100.0 KP881233.1:0-1152 A class C ADC beta-lactamase and cephalosporinase found in Acinetobacter baumannii cephalosporin
contig00016 12626 13816 adeA 0/0 100 97.7 AF370885.1:3438-4629 AdeA is the membrane fusion protein of the multidrug efflux complex AdeABC. glycylcycline, tetracycline
contig00016 9519 12626 adeB 0/0 100 97.8 AF370885.1:4628-7736 AdeB is the multidrug transporter of the adeABC efflux system. glycylcycline, tetracycline
contig00016 8045 9442 adeC 0/0 100 95.4 CP013924.1:2063742-2065140 AdeC is the outer membrane factor of the AdeABC multidrug efflux complex. It can be replaced by other outer membrane channels and is not essential for antibiotic resistance. glycylcycline, tetracycline
contig00009 68464 71643 adeF 0/0 100 100.0 CT025801.2:0-3180 AdeF is the membrane fusion protein of the multidrug efflux complex AdeFGH. fluoroquinolone, tetracycline
contig00009 71650 72870 adeG 0/0 100 100.0 CT025800.2:0-1221 AdeG is the inner membrane transporter of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00009 67003 68454 adeH 0/0 100 100.0 CT025802.2:0-1452 AdeH is the outer membrane channel protein of the AdeFGH multidrug efflux complex. fluoroquinolone, tetracycline
contig00003 41699 42949 adeI 0/0 100 100.0 CP001182.2:3283426-3284677 AdeI is the membrane fusion protein of the AdeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00003 42962 46138 adeJ 0/0 100 99.6 AY769962:2434-5611 AdeJ is a RND efflux protein that acts as the inner membrane transporter of the AdeIJK efflux complex. It has 57% identity with E. coli AcrB. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00003 46138 47592 adeK 0/0 100 98.7 AY769962:5610-7065 AdeK is the outer membrane factor protein in the adeIJK multidrug efflux complex. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00009 73086 74099 adeL 0/0 100 99.4 KR297239.1:1428-414 AdeL is a regulator of AdeFGH in Acinetobacter baumannii. AdeL mutations are associated with AdeFGH overexpression and multidrug resistance. fluoroquinolone, tetracycline
contig00012 35446 36099 adeN 0/0 100 98.0 KF147862:0-654 AdeN is a repressor of AdeIJK a RND-type efflux pump in Acinetobacter baumannii. Its inactivation increases expression of AdeJ. carbapenem, cephalosporin, diaminopyrimidine, fluoroquinolone, lincosamide, macrolide, penem, phenicol, rifamycin, tetracycline
contig00016 13962 14705 adeR 0/0 100 100.0 HM440348:0-744 AdeR is a positive regulator of AdeABC efflux system. AdeR inactivation leads to susceptibility to aminoglycoside antibiotics. glycylcycline, tetracycline
contig00016 14737 15822 adeS 0/0 100 99.7 HM440348:775-1861 AdeS is a sensor kinase in the AdeRS regulatory system of AdeABC. It is essential for AdeABC expression. glycylcycline, tetracycline
contig00037 4721 5254 ANT(2’’)-Ia 0/0 100 98.9 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig00006 209855 210679 OXA-69 0/0 100 100.0 CU459141.1:2175316-2176141 OXA-69 is a beta-lactamase found in A. baumannii cephalosporin, penam
contig00038 448 1263 sul2 0/0 100 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00037 4721 5254 (AGly)aadB 0/0 100 98.9 JQ690540:4275-4808 (AGly)aadB NA
contig00021 23924 24712 (AGly)ant(3’’)-IIa 0/0 100 98.9 NG_054648:101-889 (AGly)ant(3’’)-IIa NA
contig00011 129875 130894 (Bla)BlaA1 0/0 100 100.0 NC_010410:1803480-1804499 (Bla)BlaA1 NA
contig00004 52665 53939 (Bla)BlaA2 0/0 100 100.0 NC_010410:2507740-2509014 (Bla)BlaA2 NA
contig00002 9 1160 (Bla)blaADC-73 0/0 100 100.0 KP881233:1-1152 (Bla)blaADC-73 NA
contig00006 209855 210679 (Bla)blaOXA-69 0/0 100 100.0 AY750911:1-825 (Bla)blaOXA-69 NA
contig00006 30980 31675 (Bla)Mbl 0/0 100 100.0 NC_010410:c1997136-1996441 (Bla)Mbl NA
contig00002 315355 316317 (Bla)Zn-dependent_hydrolase 0/0 100 100.0 NC_010410:882015-882977 (Bla)Zn-dependent_hydrolase NA
contig00038 448 1263 (Sul)sul2 0/0 100 100.0 EU360945:1617-2432 (Sul)sul2 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00037 4721 5254 ant(2’’)-Ia 0/0 100 99.1 NG_052432.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig00021 23924 24712 ant(3’’)-IIa 0/0 100 100.0 NG_054646.1 aminoglycoside nucleotidyltransferase ANT(3’’)-IIa SPECTINOMYCIN, STREPTOMYCIN
contig00002 9 1160 blaADC-73 0/0 100 100.0 NG_048678.1 class C extended-spectrum beta-lactamase ADC-73 CEPHALOSPORIN
contig00006 209855 210679 blaOXA-69 0/0 100 100.0 NG_049809.1 OXA-51 family carbapenem-hydrolyzing class D beta-lactamase OXA-69 CARBAPENEM
contig00038 448 1263 sul2 0/0 100 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00004 134203 135492 ABAF 0/0 100.0 97.9 MEG_369 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAF NA
contig00011 116965 118269 ABAQ 0/0 100.0 100.0 MEG_370 Drugs:Fosfomycin:Fosfomycin_MFS_efflux_pump:ABAQ NA
contig00007 12051 13397 ABEM 0/0 100.0 98.9 MEG_372 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MATE_efflux_pumps:ABEM NA
contig00009 77408 77737 ABES 0/0 100.0 100.0 MEG_379 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:ABES NA
contig00002 9 1160 ADC 0/0 100.0 100.0 MEG_666 Drugs:betalactams:Class_C_betalactamases:ADC NA
contig00016 12626 13816 ADEA 0/0 100.0 97.7 MEG_677 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEA NA
contig00016 9519 12626 ADEB 0/0 100.0 97.8 MEG_678 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEB NA
contig00016 8045 9442 ADEC 0/0 100.0 95.4 MEG_679 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEC NA
contig00009 71650 72870 ADEF 0/0 100.0 100.0 MEG_683 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEF NA
contig00009 68464 71643 ADEG 0/0 100.0 100.0 MEG_684 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEG NA
contig00009 67003 68454 ADEH 0/0 100.0 100.0 MEG_685 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEH NA
contig00003 41699 42949 ADEI 0/0 100.0 100.0 MEG_686 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEI NA
contig00003 42962 46138 ADEJ 0/0 100.0 99.6 MEG_692 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEJ NA
contig00003 46138 47592 ADEK 0/0 100.0 99.0 MEG_696 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADEK NA
contig00009 73086 74099 ADEL 0/0 100.0 99.5 MEG_699 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEL NA
contig00012 35446 36099 ADEN 0/0 100.0 100.0 MEG_701 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADEN NA
contig00016 13962 14705 ADER 0/0 100.0 100.0 MEG_703 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADER NA
contig00016 14737 15822 ADES 0/0 100.0 99.7 MEG_704 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:ADES NA
contig00015 48180 48896 ADET2 0/0 100.0 98.9 MEG_706 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ADET2 NA
contig00012 90155 91633 AMVA 0/0 100.0 100.0 MEG_733 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_MFS_efflux_pumps:AMVA NA
contig00021 23924 24712 ANT3-DPRIME 0/0 100.0 100.0 MEG_913 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00004 52665 53939 BLAA 0/0 100.0 100.0 MEG_1247 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00011 129875 130894 BLAA 0/0 100.0 100.0 MEG_1246 Drugs:betalactams:Class_A_betalactamases:BLAA NA
contig00024 38317 39306 MEXT 0/0 100.0 98.8 MEG_3934 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_regulator:MEXT NA
contig00006 209810 210761 OXA 3/3 98.9 97.5 MEG_5236 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00038 448 1263 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
ORTHO047E
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00250 1696 2556 aac(3)-IIa_1 0/0 100.0 99.8 X51534 aac(3)-IIa Gentamicin, Tobramycin
contig00261 1539 2138 aac(6’)-Ib-cr_1 0/0 100.0 100.0 DQ303918 aac(6’)-Ib-cr Ciprofloxacin
contig00296 404 1368 ant(3’’)-Ia_1 3/7 99.3 99.1 X02340 ant(3’’)-Ia Streptomycin
contig00121 8734 9537 aph(3’’)-Ib_5 0/0 100.0 100.0 AF321551 aph(3’’)-Ib Streptomycin
contig00121 7898 8734 aph(6)-Id_1 0/0 100.0 100.0 M28829 aph(6)-Id Streptomycin
contig00121 2620 3495 blaCTX-M-15_1 0/0 100.0 100.0 AY044436 blaCTX-M-15 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Cefotaxime, Ceftazidime, Ceftriaxone, Piperacillin, Ticarcillin
contig00075 17699 18844 blaMIR-5_1 0/0 100.0 100.0 FJ237367 blaMIR-5
contig00261 578 1408 blaOXA-1_1 0/0 100.0 100.0 HQ170510 blaOXA-1 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig00121 6317 7177 blaTEM-1B_1 0/0 100.0 100.0 AY458016 blaTEM-1B Amoxicillin, Ampicillin, Cephalothin, Piperacillin, Ticarcillin
contig00313 350 1004 catA1_1 0/0 99.2 99.8 V00622 catA1 Chloramphenicol
contig00180 3154 3627 dfrA1_8 0/0 100.0 100.0 X00926 dfrA1 Trimethoprim
contig00311 442 924 dfrA14_5 0/0 100.0 99.6 DQ388123 dfrA14 Trimethoprim
contig00175 4912 5337 fosA_7 0/0 100.0 97.0 AEXB01000013 fosA Fosfomycin
contig00193 4172 5093 mph(A)_2 1/1 100.0 99.6 U36578 mph(A) Erythromycin, Azithromycin, Spiramycin, Telithromycin
contig00185 4403 5047 qnrB1_1 0/0 100.0 100.0 DQ351241 qnrB1 Ciprofloxacin
contig00180 1270 2136 sul1_5 0/0 100.0 99.9 EU780013 sul1 Sulfamethoxazole
contig00121 9598 10413 sul2_2 0/0 100.0 100.0 AY034138 sul2 Sulfamethoxazole
contig00219 1429 2697 tet(A)_6 1/22 97.8 93.2 AF534183 tet(A) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00250 1696 2556 AAC(3)-IIe 0/0 100.0 99.5 EU022315.1:0-861 AAC(3)-IIe is a plasmid-encoded aminoglycoside acetyltransferase in E. coli aminoglycoside
contig00261 1539 2138 AAC(6’)-Ib-cr 0/0 100.0 100.0 DQ303918:0-600 AAC(6’)-Ib-cr is an aminoglycoside acetyltransferase encoded by plasmids transposons integrons in Enterobacteriaceae. The aac(6’)-Ib-cr variant gene can induce resistance against aminoglycoside and fluoroquinolone simultaneously aminoglycoside, fluoroquinolone
contig00296 404 1368 ANT(3’’)-IIa 3/7 99.3 99.1 X02340.1:222-1194 ANT(3’’)-IIa is a aminoglycoside nucleotidyltransferase identified in Acinetobacter spp. via horizontal gene transfer mechanisms. aminoglycoside
contig00121 8734 9537 APH(3’’)-Ib 0/0 100.0 99.8 AF313472:15593-16397 APH(3’’)-Ib is an aminoglycoside phosphotransferase encoded by plasmids transposons integrative conjugative elements and chromosomes in Enterobacteriaceae and Pseudomonas spp. aminoglycoside
contig00121 7898 8734 APH(6)-Id 0/0 100.0 99.9 AF024602:3155-3992 APH(6)-Id is an aminoglycoside phosphotransferase encoded by plasmids integrative conjugative elements and chromosomal genomic islands in K. pneumoniae Salmonella spp. E. coli Shigella flexneri Providencia alcalifaciens Pseudomonas spp. V. cholerae Edwardsiella tarda Pasteurella multocida and Aeromonas bestiarum aminoglycoside
contig00313 350 1004 catI 0/0 99.2 99.8 V00622:243-903 catI is a chromosome and transposon-encoded variant of the cat gene found in Escherichia coli and Acinetobacter baumannii phenicol
contig00121 2620 3495 CTX-M-15 0/0 100.0 100.0 AY044436:1435-2311 CTX-M-15 is a beta-lactamase found in the Enterobacteriaceae family cephalosporin
contig00180 3154 3627 dfrA1 0/0 100.0 99.8 KJ541681.1:19526-20000 dfrA1 is an integron-encoded dihydrofolate reductase diaminopyrimidine
contig00311 442 924 dfrA14 0/0 100.0 99.8 EU780012:2162-2645 dfrA14 is an integron-encoded dihydrofolate reductase found in Escherichia coli diaminopyrimidine
contig00104 6740 7933 Enterobacter_cloacae_acrA 0/0 100.0 99.6 DQ679966:299-1493 AcrA is a subunit of the AcrAB-TolC multidrug efflux system that in E. cloacae. cephalosporin, fluoroquinolone, glycylcycline, penam, phenicol, rifamycin, tetracycline, triclosan
contig00175 4912 5337 FosA2 0/0 100.0 92.2 EU487198:216-642 An enzyme that confers resistance to fosfomycin in Enterobacter cloacae by breaking the epoxide ring of the molecule. It depends on the cofactors Manganese (II) and Potassium and uses Glutathione (GSH) as the nucleophilic molecule. fosfomycin
contig00075 17699 18844 MIR-23 0/0 100.0 99.7 KJ949106.1:0-1146 MIR-23 originally described as AZECL-25 is a class C beta-lactamase that is found in Enterobacter cloacae. cephalosporin, monobactam
contig00193 4172 5077 mphA 0/0 100.0 99.9 D16251.1:2531-1625 The mphA gene encodes for resistance enzyme MPH(2’)-I which preferentially inactivate 14-membered macrolides (e.g.erythromycin telithromycin roxithromycin) over 16-membered macrolides (e.g.tylosin spiramycin). It phosphorylates macrolides at 2’-OH hydroxyl of desosamine sugar of macrolides in a GTP-dependent manner. macrolide
contig00261 578 1408 OXA-1 0/0 100.0 100.0 JN420336.1:2230-1399 OXA-1 is a beta-lactamase found in E. coli cephalosporin, penam
contig00223 725 1057 qacH 0/0 100.0 99.7 DQ149925.1:188-521 qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae fluoroquinolone
contig00185 4366 5047 QnrB17 1/1 100.0 99.1 AM919398:0-681 QnrB17 is a plasmid-mediated quinolone resistance protein found in Citrobacter freundii fluoroquinolone
contig00066 19789 20140 ramA 0/0 93.9 93.2 JQ727668:0-375 RamA (resistance antibiotic multiple) is a positive regulator of AcrAB-TolC and leads to high level multidrug resistance in Klebsiella pneumoniae Salmonella enterica and Enterobacter aerugenes increasing the expression of both the mar operon as well as AcrAB. RamA also decreases OmpF expression. carbapenem, cephalosporin, cephamycin, fluoroquinolone, glycylcycline, monobactam, penam, penem, phenicol, rifamycin, tetracycline, triclosan
contig00180 3754 4611 RSA-1 0/0 100.0 99.8 MG739510.1:0-858 RSA-1 is a class A beta-lactamase resistance enzyme identified from a functional metagenomic study of contaminated river sediments. carbapenem, cephalosporin
contig00180 1270 2109 sul1 0/0 100.0 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00121 9598 10413 sul2 0/0 100.0 100.0 AY055428.1:21084-20268 Sul2 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria usually found on small plasmids. sulfonamide
contig00121 6317 7177 TEM-1 0/0 100.0 99.9 AL513383:161910-162771 TEM-1 is a broad-spectrum beta-lactamase found in many Gram-negative bacteria. Confers resistance to penicillins and first generation cephalosphorins. cephalosporin, monobactam, penam, penem
contig00219 1429 2697 tet(A) 1/22 97.8 93.2 AF534183.1:2970-4245 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00250 1696 2556 (AGly)aac3-IIa 0/0 100.0 99.8 X51534:91-951 (AGly)aac3-IIa NA
contig00296 404 1215 (AGly)aadA1-pm 0/0 97.7 99.9 JQ690540:7968-8798 (AGly)aadA1-pm NA
contig00121 8734 9537 (AGly)strA 0/0 100.0 99.9 AB366441:22458-23261 (AGly)strA NA
contig00121 7898 8734 (AGly)strB 0/0 100.0 100.0 FJ474091:264-1100 (AGly)strB NA
contig00121 2620 3495 (Bla)blaCTX-M-15 0/0 100.0 100.0 JQ686199:261-1136 (Bla)blaCTX-M-15 NA
contig00075 17699 18844 (Bla)blaMIR-5 0/0 100.0 100.0 FJ237367:1-1146 (Bla)blaMIR-5 NA
contig00261 578 1408 (Bla)blaOXA-1 0/0 100.0 100.0 JQ682867:1-831 (Bla)blaOXA-1 NA
contig00121 6317 7177 (Bla)blaTEM-105 0/0 100.0 99.9 AF516720:215-1075 (Bla)blaTEM-105 NA
contig00175 4912 5337 (Fcyn)FosA2 0/0 100.0 92.2 EU487198:217-642 (Fcyn)FosA2 NA
contig00185 4366 5047 (Flq)qnrB1 1/1 100.0 99.8 DQ351241:1-681 (Flq)qnrB1 NA
contig00193 4172 5077 (MLS)mph(A) 0/0 100.0 99.9 DQ445270:1626-2531 (MLS)mph(A) NA
contig00313 350 1004 (Phe)catA1 0/0 99.2 99.8 V00622:244-903 (Phe)catA1 NA
contig00180 1270 2109 (Sul)sul1 0/0 100.0 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig00121 9598 10413 (Sul)sul2 0/0 100.0 100.0 EU360945:1617-2432 (Sul)sul2 NA
contig00219 1429 2725 (Tet)tetA 1/22 100.0 93.3 JX424423:94438-95712 (Tet)tetA NA
contig00219 757 1398 (Tet)tetR 1/9 98.6 93.1 HF545434:53576-54226 (Tet)tetR NA
contig00180 3154 3627 (Tmt)dfrA1 0/0 100.0 100.0 JQ794607:474 (Tmt)dfrA1 NA
contig00311 442 915 (Tmt)dfrA14 0/0 100.0 100.0 GU726917:72-545 (Tmt)dfrA14 NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00250 1696 2556 aac(3)-IIe 0/0 100.0 99.8 NG_047244.1 aminoglycoside N-acetyltransferase AAC(3)-IIe GENTAMICIN
contig00261 1539 2093 aac(6’)-Ib-D181Y 0/0 100.0 99.8 NG_067946.1 AAC(6’)-Ib family aminoglycoside 6’-N-acetyltransferase AMIKACIN, KANAMYCIN, TOBRAMYCIN
contig00296 404 1195 aadA1 0/0 100.0 100.0 NG_052536.1 ANT(3’’)-Ia family aminoglycoside nucleotidyltransferase AadA1 STREPTOMYCIN
contig00121 8734 9561 aph(3’’)-Ib 0/0 100.0 100.0 NG_056002.2 aminoglycoside O-phosphotransferase APH(3’’)-Ib STREPTOMYCIN
contig00121 7898 8734 aph(6)-Id 0/0 100.0 100.0 NG_047464.1 aminoglycoside O-phosphotransferase APH(6)-Id STREPTOMYCIN
contig00121 2620 3495 blaCTX-M-15 0/0 100.0 100.0 NG_048935.1 class A extended-spectrum beta-lactamase CTX-M-15 CEPHALOSPORIN
contig00075 17699 18844 blaMIR-5 0/0 100.0 100.0 NG_049306.1 cephalosporin-hydrolyzing class C beta-lactamase MIR-5 CEPHALOSPORIN
contig00261 578 1408 blaOXA-1 0/0 100.0 100.0 NG_049392.1 oxacillin-hydrolyzing class D beta-lactamase OXA-1 CEPHALOSPORIN
contig00121 6317 7177 blaTEM-1 0/0 100.0 100.0 NG_050145.1 class A broad-spectrum beta-lactamase TEM-1 BETA-LACTAM
contig00313 350 1004 catA1 0/0 99.2 99.8 NG_047582.1 type A-1 chloramphenicol O-acetyltransferase CHLORAMPHENICOL
contig00180 3154 3627 dfrA1 0/0 100.0 100.0 NG_047676.1 trimethoprim-resistant dihydrofolate reductase DfrA1 TRIMETHOPRIM
contig00311 442 915 dfrA14 0/0 100.0 100.0 NG_056035.1 trimethoprim-resistant dihydrofolate reductase DfrA14 TRIMETHOPRIM
contig00175 4912 5337 fosA 0/0 100.0 96.5 NG_050405.1 fosfomycin resistance glutathione transferase FosA FOSFOMYCIN
contig00193 4172 5093 mph(A) 1/1 100.0 99.6 NG_047986.1 Mph(A) family macrolide 2’-phosphotransferase MACROLIDE
contig00053 19028 22147 oqxB9 0/0 99.0 90.2 NG_050458.1 multidrug efflux RND transporter permease subunit OqxB9 PHENICOL, QUINOLONE
contig00185 4403 5047 qnrB1 0/0 100.0 100.0 NG_050469.1 quinolone resistance pentapeptide repeat protein QnrB1 QUINOLONE
contig00180 1270 2109 sul1 0/0 100.0 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig00121 9598 10413 sul2 0/0 100.0 100.0 NG_051852.1 sulfonamide-resistant dihydropteroate synthase Sul2 SULFONAMIDE
contig00219 1526 2725 tet(A) 0/0 100.0 100.0 NG_048157.1 tetracycline efflux MFS transporter Tet(A) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00250 1696 2556 AAC3 0/0 100.0 99.8 MEG_44 Drugs:Aminoglycosides:Aminoglycoside_N-acetyltransferases:AAC3 NA
contig00104 6740 7933 ACRB 0/0 100.0 99.6 MEG_402 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:ACRB NA
contig00296 404 1368 ANT3-DPRIME 3/7 99.3 99.1 MEG_949 Drugs:Aminoglycosides:Aminoglycoside_O-nucleotidyltransferases:ANT3-DPRIME NA
contig00121 8734 9561 APH3-DPRIME 0/0 100.0 100.0 MEG_1019 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH3-DPRIME NA
contig00121 7898 8734 APH6 0/0 100.0 100.0 MEG_1086 Drugs:Aminoglycosides:Aminoglycoside_O-phosphotransferases:APH6 NA
contig00313 339 1004 CATA 0/0 99.2 100.0 MEG_1593 Drugs:Phenicol:Chloramphenicol_acetyltransferases:CATA NA
contig00320 62 1004 CTX 0/0 100.0 99.0 MEG_2435 Drugs:betalactams:Class_A_betalactamases:CTX NA
contig00180 3154 3627 DFRA 0/0 100.0 99.8 MEG_2495 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00311 442 915 DFRA 0/0 100.0 99.8 MEG_2517 Drugs:Trimethoprim:Dihydrofolate_reductase:DFRA NA
contig00175 4912 5493 FOSA 0/0 100.0 92.8 MEG_2990 Drugs:Fosfomycin:Fosfomycin_thiol_transferases:FOSA NA
contig00075 17699 18844 MIR 0/0 100.0 100.0 MEG_3959 Drugs:betalactams:Class_C_betalactamases:MIR NA
contig00193 4172 5093 MPHA 1/1 100.0 99.6 MEG_4030 Drugs:MLS:Macrolide_phosphotransferases:MPHA NA
contig00053 19028 22147 OQXB 0/0 99.0 90.2 MEG_4359 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:OQXB NA
contig00261 578 1408 OXA 0/0 100.0 100.0 MEG_4980 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00223 725 1057 QACF 0/0 100.0 100.0 MEG_5833 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACF NA
contig00185 4366 5047 QNRB 1/1 100.0 99.1 MEG_5928 Drugs:Fluoroquinolones:Quinolone_resistance_protein_Qnr:QNRB NA
contig00066 19789 20140 RAMA 0/0 93.9 93.2 MEG_6044 Drugs:Multi-drug_resistance:Multi-drug_RND_efflux_regulator:RAMA NA
contig00180 3754 4611 RSA 0/0 100.0 99.8 MEG_6149 Drugs:betalactams:Class_A_betalactamases:RSA NA
contig00180 1143 2110 SULI 0/0 100.0 100.0 MEG_6615 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI NA
contig00121 9598 10413 SULII 0/0 100.0 100.0 MEG_6617 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULII NA
contig00121 5950 7195 TEM 0/0 98.3 99.4 MEG_6875 Drugs:betalactams:Class_A_betalactamases:TEM NA
contig00219 1526 2725 TETA 0/0 100.0 100.0 MEG_7021 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA NA
ORTHO05E
Resfinder
## [1] "No antibiotic resistance genes from Resfinder database were found"
CARD
## [1] "No antibiotic resistance genes from CARD database were found"
ARG-ANNOT
## [1] "No antibiotic resistance genes from ARG-ANNOT database were found"
NCBI
## [1] "No antibiotic resistance genes from NCBI database were found"
MEGARES
## [1] "No antibiotic resistance genes from MEGARES database were found"
ORTHO082EII
Resfinder
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00278 783 1316 ant(2’’)-Ia_1 0/0 100.0 100.0 X04555 ant(2’’)-Ia Gentamicin, Tobramycin
contig00278 14 769 blaDIM-1_1 0/0 100.0 100.0 GU323019 blaDIM-1
contig02287 111 928 blaOXA-22_1 0/0 99.2 100.0 AF064820 blaOXA-22 Amoxicillin, Ampicillin, Aztreonam, Cefepime, Piperacillin, Piperacillin+Tazobactam
contig01918 45 860 blaOXA-60_1 0/0 100.0 100.0 AF525303 blaOXA-60 Amoxicillin, Amoxicillin+Clavulanic_acid, Ampicillin, Ampicillin+Clavulanic_acid, Imipenem
contig01154 204 1463 cmlA1_1 0/0 100.0 99.8 M64556 cmlA1 Chloramphenicol
contig00362 1 817 sul1_2 0/0 97.3 100.0 U12338 sul1 Sulfamethoxazole
contig00005 833 2079 tet(A)_6 0/0 97.8 100.0 AF534183 tet(A) Doxycycline, Tetracycline
contig00462 874 2049 tet(G)_2 0/0 100.0 99.9 AF133140 tet(G) Doxycycline, Tetracycline
CARD
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00278 783 1316 ANT(2’’)-Ia 0/0 100.0 100.0 AF078527:3769-4303 Plasmid or integron-encoded nucleotidylylation of 2-deoxystreptamine aminoglycosides at the hydroxyl group at position 2’’ in P. aeruginosa K. pneumoniae Morganella morganii E. coli S. typhimurium C. freundii and A. baumannii aminoglycoside
contig02083 33 485 arr-2 0/0 100.0 100.0 AF078527:4387-4840 arr-2 is an integron-encoded ribosyltransferase found in Pseudomonas aeruginosa rifamycin
contig01154 204 1463 cmlA6 0/0 100.0 100.0 AF294653:2749-4009 cmlA6 is a plasmid-encoded chloramphenicol exporter that is found in Pseudomonas aeruginosa phenicol
contig00278 14 769 DIM-1_beta-lactamase 0/0 100.0 100.0 KC004136:40-796 Dutch imipenemase or DIM-1 is an integron-encoded metallo-beta-lactamase from Pseudomonas stutzeri carbapenem, cephalosporin
contig02287 111 928 OXA-22 0/0 99.2 100.0 AF064820:951-1776 OXA-22 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig01918 45 860 OXA-60 0/0 100.0 100.0 AF525303:2770-3586 OXA-60 is a beta-lactamase found in Ralstonia pickettii cephalosporin, penam
contig00278 1479 1811 qacH 0/0 100.0 91.6 DQ149925.1:188-521 qacH is a subunit of the qac multidrug efflux pump in Vibrio cholerae fluoroquinolone
contig00362 1 817 sul1 0/0 97.3 100.0 JF969163:1053-1893 Sul1 is a sulfonamide resistant dihydropteroate synthase of Gram-negative bacteria. It is linked to other resistance genes of class 1 integrons. sulfonamide
contig00005 833 2079 tet(A) 0/0 97.8 100.0 AF534183.1:2970-4245 TetA is a tetracycline efflux pump found in many species of Gram-negative bacteria. tetracycline
contig00462 874 2049 tet(G) 0/0 100.0 92.9 AF133139:0-1176 TetG is a tetracycline efflux protein found in Gram-negative bacteria. The encoding gene is found in both chromosomal and plasmid DNA where it is frequently linked to the floR sul1 and cmlA9 genes which encode proteins that can confer florfenicol/chloramphenicol sulfamethoxazole and chloramphenicol resistance respectively. tetracycline
ARG-ANNOT
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00278 783 1316 (AGly)aadB 0/0 100.0 100.0 JQ690540:4275-4808 (AGly)aadB NA
contig00278 14 769 (Bla)blaDIM-1 0/0 100.0 100.0 GU323019:1-756 (Bla)blaDIM-1 NA
contig02287 111 928 (Bla)blaOXA-22 0/0 99.2 100.0 AF064820:952-1776 (Bla)blaOXA-22 NA
contig01918 45 860 (Bla)blaOXA-60 0/0 100.0 93.1 AY664505:1-816 (Bla)blaOXA-60 NA
contig01154 204 1463 (Phe)cmlA6 0/0 100.0 100.0 NG_047655:101-1360 (Phe)cmlA6 NA
contig02083 33 485 (Rif)arr2 0/0 100.0 100.0 JQ639792:1050-1502 (Rif)arr2 NA
contig00362 1 817 (Sul)sul1 0/0 97.3 100.0 AF071413:6700-7539 (Sul)sul1 NA
contig00005 833 2107 (Tet)tetA 0/0 100.0 100.0 JX424423:94438-95712 (Tet)tetA NA
contig00462 874 2049 (Tet)tetG 0/0 100.0 99.9 AF133140:757-1932 (Tet)tetG NA
contig00005 152 802 (Tet)tetR 0/0 100.0 100.0 HF545434:53576-54226 (Tet)tetR NA
contig00462 2153 2761 (Tet)tetR(G) 0/0 96.2 98.5 S52438:113-745 (Tet)tetR(G) NA
NCBI
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig00278 783 1316 ant(2’’)-Ia 0/0 100.0 100.0 NG_047387.1 aminoglycoside nucleotidyltransferase ANT(2’’)-Ia GENTAMICIN, KANAMYCIN, TOBRAMYCIN
contig02083 33 485 arr-2 0/0 100.0 100.0 NG_048580.1 NAD(+)–rifampin ADP-ribosyltransferase Arr-2 RIFAMYCIN
contig00278 14 769 blaDIM-1 0/0 100.0 100.0 NG_049077.1 subclass B1 metallo-beta-lactamase DIM-1 CARBAPENEM
contig02287 111 928 blaOXA-22 0/0 99.2 100.0 NG_049518.1 benzylpenicillin-hydrolyzing class D beta-lactamase OXA-22 BETA-LACTAM
contig01918 45 860 blaOXA-60 0/0 100.0 100.0 NG_049800.1 carbapenem-hydrolyzing class D beta-lactamase OXA-60 CARBAPENEM
contig01154 204 1463 cmlA6 0/0 100.0 100.0 NG_047655.1 chloramphenicol efflux MFS transporter CmlA6 CHLORAMPHENICOL
contig00462 2986 4200 floR2 0/0 100.0 100.0 NG_047875.1 chloramphenicol/florfenicol efflux MFS transporter FloR2 CHLORAMPHENICOL, FLORFENICOL
contig00362 1 817 sul1 0/0 97.3 100.0 NG_048082.1 sulfonamide-resistant dihydropteroate synthase Sul1 SULFONAMIDE
contig00005 908 2107 tet(A) 0/0 100.0 100.0 NG_048154.1 tetracycline efflux MFS transporter Tet(A) TETRACYCLINE
contig00462 874 2049 tet(G) 0/0 100.0 99.9 NG_051907.1 tetracycline efflux MFS transporter Tet(G) TETRACYCLINE
MEGARES
Contig Start End Gene Gaps Coverage Identity Accession Product Resistance
contig01154 3 1463 CMLA 1/1 100.0 99.6 MEG_1768 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:CMLA NA
contig00278 14 769 DIM 0/0 100.0 100.0 MEG_2649 Drugs:betalactams:Class_B_betalactamases:DIM NA
contig00462 2986 4200 FLOR 0/0 100.0 100.0 MEG_2912 Drugs:Phenicol:Phenicol_resistance_MFS_efflux_pumps:FLOR NA
contig01918 45 860 OXA 0/0 100.0 100.0 MEG_4779 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig02287 111 928 OXA 0/0 99.2 100.0 MEG_4766 Drugs:betalactams:Class_D_betalactamases:OXA NA
contig00278 1479 1811 QACL 0/0 100.0 100.0 MEG_5852 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_SMR_efflux_pumps:QACL NA
contig00362 1 944 SULI 0/0 97.5 100.0 MEG_6615 Drugs:Sulfonamides:Sulfonamide-resistant_dihydropteroate_synthases:SULI NA
contig00005 833 2107 TETA 0/0 100.0 100.0 MEG_7024 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETA NA
contig00462 874 2049 TETG 0/0 100.0 99.9 MEG_7077 Drugs:Tetracyclines:Tetracycline_resistance_MFS_efflux_pumps:TETG NA
contig00079 8019 9173 TTGA 0/0 100.0 90.0 MEG_7287 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:TTGA NA
contig00079 9177 12329 TTGB 0/0 100.0 92.0 MEG_7288 Multi-compound:Drug_and_biocide_resistance:Drug_and_biocide_RND_efflux_pumps:TTGB NA


Summary figures

Presence/Absence of antibiotic resistance genes (coverage and identity > 90%) on each sample

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CARD
ARG-ANNOT
NCBI
MEGARES


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Plasmid Profiling


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Gaps Gaps in subject (genome) and query (antibiotic resistance gene)
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


Select sample

ID003II
## [1] "NO PLASMID FOUND!!"
ID012II
## [1] "NO PLASMID FOUND!!"
ID014II
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00364 768 1155 IncFIA_1 0/0 100 99.7 AP001918 IncFIA_1__AP001918
contig00403 832 1513 IncFIB(AP001918)_1 0/0 100 98.2 AP001918 IncFIB(AP001918)_1__AP001918
ID030
## [1] "NO PLASMID FOUND!!"
ID063
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00085 400 632 Col(BS512)_1 0/0 100 100.0 NC_010656 Col(BS512)_1__NC_010656
contig00090 1071 1332 Col(MG828)_1 0/0 100 93.1 NC_008486 Col(MG828)_1__NC_008486
contig00067 5514 5644 ColRNAI_1 1/1 100 90.1 DQ298019 ColRNAI_1__DQ298019
contig00068 3818 4582 IncY_1 0/0 100 98.8 K02380 IncY_1__K02380
ID089
## [1] "NO PLASMID FOUND!!"
ID186
## [1] "NO PLASMID FOUND!!"
ID259
## [1] "NO PLASMID FOUND!!"
ORTHO015E
## [1] "NO PLASMID FOUND!!"
ORTHO037E
## [1] "NO PLASMID FOUND!!"
ORTHO047E
Contig Start End Gene Gaps Coverage Identity Accession Product
contig00003 81165 81491 IncHI2_1 0/0 100 100.0 BX664015 IncHI2_1__BX664015
contig00003 96357 96986 IncHI2A_1 0/0 100 100.0 BX664015 IncHI2A_1__BX664015
contig00149 883 1133 IncR_1 0/0 100 99.6 DQ449578 IncR_1__DQ449578
ORTHO05E
## [1] "NO PLASMID FOUND!!"
ORTHO082EII
## [1] "NO PLASMID FOUND!!"


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Virulence Factor Determination


Field Description
Contig Contig name where the gene was found
Start Start position of the gene within the contig
End End position of the gene within the contig
Gene Antibiotic resistance gene
Coverage Proportion (%) of the gene covered
Identity Proportion (%) of exact nucleotide matches
Accession Accesion number of the antibiotic resistance gene
Product Antibiotic resistance gene product


Select the sample

ID003II
## Error in read.table("ID003II_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(vfdb): object 'vfdb' not found
## Error in cbind(vfdb[, 1:9]): object 'vfdb' not found
## Error in colnames(vfdbdata) = c("Contig", "Start", "End", "Strand", "Gene", : object 'vfdbdata' not found
## Error in eval(expr, envir, enclos): object 'vfdb' not found
## Error in row.names(vfdb) = NULL: object 'vfdb' not found
## Error in nrow(vfdb): object 'vfdb' not found
ID012II
## Error in read.table("ID012II_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
## Error in as.data.frame(vfdb): object 'vfdb' not found
## Error in cbind(vfdb[, 1:9]): object 'vfdb' not found
## Error in colnames(vfdbdata) = c("Contig", "Start", "End", "Strand", "Gene", : object 'vfdbdata' not found
## Error in eval(expr, envir, enclos): object 'vfdb' not found
## Error in row.names(vfdb) = NULL: object 'vfdb' not found
## Error in nrow(vfdb): object 'vfdb' not found
ID014II
Contig Start End Strand Gene Coverage Identity Accession Product
contig00017 34037 35465 - aslA 100.0 93.6 AAG10151 (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00179 6301 6756 - csgB 99.8 83.8 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 7511 8161 + csgD 100.0 81.1 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 8580 8996 + csgF 99.0 81.2 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 9023 9856 + csgG 100.0 83.5 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00088 15712 16458 - entA 100.0 95.7 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 16458 17315 - entB 100.0 98.1 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 18949 20136 - entC 100.0 97.9 NP_752611 (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00320 107 877 - entD 100.0 95.2 NP_752599 (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 17329 18939 - entE 100.0 95.5 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 26999 30196 - entF 82.4 95.5 NP_752604 (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 21459 22709 - entS 100.0 95.4 NP_752609 (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00184 2194 4093 + espL1 100.0 97.6 NP_288154 (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00072 27898 30084 + espL4 100.0 97.3 NP_290644 (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00116 21550 22603 + espR1 83.7 93.8 NP_287686 (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00194 10350 11484 + espR4 99.5 84.3 NP_288396 (espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00065 33331 34752 - espX1 100.0 93.2 NP_285716 (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00251 287 1867 + espX4 99.9 93.2 NP_290672 (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00238 7154 8446 - espX5 100.0 97.1 NP_290699 (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00039 24795 25606 - espY1 99.9 87.0 NP_285753 (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00320 902 3142 - fepA 100.0 96.7 NP_752600 (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 20499 21455 + fepB 100.0 97.5 NP_752610 (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 24810 25625 + fepC 100.0 97.3 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 22808 23824 + fepD 100.0 96.1 NP_752608 (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 23821 24813 + fepG 100.0 94.1 NP_752607 (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00320 3385 4587 + fes 100.0 96.7 NP_752602 (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00100 25238 25849 - fimA 100.0 88.6 NP_757241 (fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00270 1070 1672 - fimB 100.0 98.2 NP_757239 (fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 23872 24597 - fimC 100.0 98.9 NP_757243 (fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 21169 23805 - fimD 100.0 98.6 NP_757244 (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00270 1 593 - fimE 99.3 99.3 NP_757240 (fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 20629 21162 - fimF 100.0 97.9 NP_757245 (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 20113 20616 - fimG 100.0 97.8 NP_757247 (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 19191 20102 - fimH 100.0 97.4 NP_757248 (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 24634 25173 - fimI 100.0 98.7 NP_757242 (fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00230 2728 4749 + fyuA 100.0 99.9 NP_405467 (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016 7662 8492 + gspC 100.0 94.7 YP_404599 (gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 8732 10582 + gspD 100.0 96.1 YP_404600 (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 10582 12075 + gspE 100.0 96.9 YP_404601 (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 12075 13274 + gspF 100.0 96.0 YP_404602 (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 13315 13770 + gspG 100.0 95.0 YP_404603 (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 13807 14336 + gspH 99.8 94.9 YP_404604 (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 14333 14704 + gspI 100.0 94.9 YP_404605 (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 14737 15306 + gspJ 100.0 96.7 YP_404606 (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 15303 16280 + gspK 100.0 97.0 YP_404607 (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 16595 17455 + gspL 100.0 97.0 YP_404608 (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 17571 17993 + gspM 100.0 98.3 YP_404609 (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00109 15615 21722 + irp2 100.0 99.8 NP_405472 (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00300 4506 5546 - ompA 100.0 98.1 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00109 14465 15424 + ybtA 100.0 99.5 NP_405473 (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00230 1020 2597 + ybtE 100.0 99.8 NP_405468 (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 12496 14298 - ybtP 100.0 99.6 NP_405474 (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 10707 12509 - ybtQ 100.0 99.7 NP_405475 (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 8102 9406 - ybtS 100.0 99.9 NP_405477 (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00230 213 1016 + ybtT 100.0 99.8 NP_405469 (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 9434 10714 - ybtX 100.0 99.7 NP_405476 (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
ID030
## Error in read.table("ID030_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00017 34037 35465 - aslA 100.0 93.6 AAG10151 (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00179 6301 6756 - csgB 99.8 83.8 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 7511 8161 + csgD 100.0 81.1 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 8580 8996 + csgF 99.0 81.2 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00179 9023 9856 + csgG 100.0 83.5 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00088 15712 16458 - entA 100.0 95.7 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 16458 17315 - entB 100.0 98.1 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 18949 20136 - entC 100.0 97.9 NP_752611 (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00320 107 877 - entD 100.0 95.2 NP_752599 (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 17329 18939 - entE 100.0 95.5 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 26999 30196 - entF 82.4 95.5 NP_752604 (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 21459 22709 - entS 100.0 95.4 NP_752609 (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00184 2194 4093 + espL1 100.0 97.6 NP_288154 (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00072 27898 30084 + espL4 100.0 97.3 NP_290644 (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00116 21550 22603 + espR1 83.7 93.8 NP_287686 (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00194 10350 11484 + espR4 99.5 84.3 NP_288396 (espR4) Type III secretion system effector espR4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00065 33331 34752 - espX1 100.0 93.2 NP_285716 (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00251 287 1867 + espX4 99.9 93.2 NP_290672 (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00238 7154 8446 - espX5 100.0 97.1 NP_290699 (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00039 24795 25606 - espY1 99.9 87.0 NP_285753 (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00320 902 3142 - fepA 100.0 96.7 NP_752600 (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 20499 21455 + fepB 100.0 97.5 NP_752610 (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 24810 25625 + fepC 100.0 97.3 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 22808 23824 + fepD 100.0 96.1 NP_752608 (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00088 23821 24813 + fepG 100.0 94.1 NP_752607 (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00320 3385 4587 + fes 100.0 96.7 NP_752602 (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00100 25238 25849 - fimA 100.0 88.6 NP_757241 (fimA) Type-1 fimbrial protein A chain precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00270 1070 1672 - fimB 100.0 98.2 NP_757239 (fimB) Type 1 fimbriae Regulatory protein fimB [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 23872 24597 - fimC 100.0 98.9 NP_757243 (fimC) Chaperone protein fimC precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 21169 23805 - fimD 100.0 98.6 NP_757244 (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00270 1 593 - fimE 99.3 99.3 NP_757240 (fimE) Type 1 fimbriae Regulatory protein fimE [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 20629 21162 - fimF 100.0 97.9 NP_757245 (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 20113 20616 - fimG 100.0 97.8 NP_757247 (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 19191 20102 - fimH 100.0 97.4 NP_757248 (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00100 24634 25173 - fimI 100.0 98.7 NP_757242 (fimI) Fimbrin-like protein fimI precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00230 2728 4749 + fyuA 100.0 99.9 NP_405467 (fyuA) pesticin/yersiniabactin receptor protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00016 7662 8492 + gspC 100.0 94.7 YP_404599 (gspC) general secretion pathway protein C [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 8732 10582 + gspD 100.0 96.1 YP_404600 (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 10582 12075 + gspE 100.0 96.9 YP_404601 (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 12075 13274 + gspF 100.0 96.0 YP_404602 (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 13315 13770 + gspG 100.0 95.0 YP_404603 (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 13807 14336 + gspH 99.8 94.9 YP_404604 (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 14333 14704 + gspI 100.0 94.9 YP_404605 (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 14737 15306 + gspJ 100.0 96.7 YP_404606 (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 15303 16280 + gspK 100.0 97.0 YP_404607 (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 16595 17455 + gspL 100.0 97.0 YP_404608 (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00016 17571 17993 + gspM 100.0 98.3 YP_404609 (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00109 15615 21722 + irp2 100.0 99.8 NP_405472 (irp2) yersiniabactin biosynthetic protein Irp2 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00300 4506 5546 - ompA 100.0 98.1 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00109 14465 15424 + ybtA 100.0 99.5 NP_405473 (ybtA) transcriptional regulator YbtA [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00230 1020 2597 + ybtE 100.0 99.8 NP_405468 (ybtE) yersiniabactin siderophore biosynthetic protein [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 12496 14298 - ybtP 100.0 99.6 NP_405474 (ybtP) lipoprotein inner membrane ABC-transporter [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 10707 12509 - ybtQ 100.0 99.7 NP_405475 (ybtQ) inner membrane ABC-transporter YbtQ [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 8102 9406 - ybtS 100.0 99.9 NP_405477 (ybtS) salicylate synthase Irp9 [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00230 213 1016 + ybtT 100.0 99.8 NP_405469 (ybtT) yersiniabactin biosynthetic protein YbtT [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
contig00109 9434 10714 - ybtX 100.0 99.7 NP_405476 (ybtX) putative signal transducer [Yersiniabactin (VF0136)] [Yersinia pestis CO92]
ID063
Contig Start End Strand Gene Coverage Identity Accession Product
contig00023 35665 37093 + aslA 100.0 92.9 AAG10151 (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005 153477 153932 + csgB 99.8 83.6 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 152072 152722 - csgD 100.0 81.3 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 151237 151653 - csgF 99.0 81.2 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 150377 151210 - csgG 100.0 83.5 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012 99370 100116 - entA 100.0 95.7 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00099 257 1003 + entA 100.0 98.4 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100116 100973 - entB 100.0 98.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 102607 103794 - entC 100.0 97.9 NP_752611 (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 105 875 - entD 100.0 95.2 NP_752599 (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100987 102597 - entE 100.0 95.4 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 4803 8656 + entF 99.3 95.6 NP_752604 (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 105117 106367 - entS 100.0 95.4 NP_752609 (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003 88782 90681 - espL1 100.0 97.6 NP_288154 (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 88201 90387 + espL4 100.0 97.3 NP_290644 (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015 12139 13193 - espR1 83.7 94.1 NP_287686 (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 102593 104013 + espX1 99.9 95.3 NP_285716 (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 58405 59985 - espX4 100.0 96.5 NP_290672 (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 27599 28891 + espX5 100.0 97.0 NP_290699 (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 63516 64327 - espY1 99.9 87.0 NP_285753 (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006 78302 82550 - fdeC 99.9 94.2 YP_002390132 (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00066 900 3140 - fepA 100.0 96.7 NP_752600 (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 104157 105113 + fepB 100.0 97.5 NP_752610 (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 108468 109283 + fepC 100.0 97.3 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 106466 107482 + fepD 100.0 96.1 NP_752608 (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 107479 108471 + fepG 100.0 94.1 NP_752607 (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 3383 4585 + fes 100.0 96.7 NP_752602 (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00050 21169 23555 - fimD 90.5 98.7 NP_757244 (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20629 21162 - fimF 100.0 97.9 NP_757245 (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20113 20616 - fimG 100.0 97.8 NP_757247 (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 19191 20102 - fimH 100.0 97.5 NP_757248 (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035 903 2753 + gspD 100.0 97.0 YP_404600 (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 2753 4246 + gspE 100.0 96.5 YP_404601 (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 4246 5445 + gspF 100.0 96.0 YP_404602 (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5486 5941 + gspG 100.0 95.0 YP_404603 (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5978 6508 + gspH 100.0 95.3 YP_404604 (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6505 6876 + gspI 100.0 95.2 YP_404605 (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6909 7478 + gspJ 100.0 96.7 YP_404606 (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 7475 8452 + gspK 100.0 96.7 YP_404607 (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 8767 9627 + gspL 100.0 97.1 YP_404608 (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 9743 10165 + gspM 100.0 97.9 YP_404609 (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005 69490 70530 - ompA 100.0 98.1 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006 91657 92410 + yagV/ecpE 99.7 97.1 NP_286006 (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 90090 91733 + yagW/ecpD 100.0 99.1 NP_286007 (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 87575 90100 + yagX/ecpC 100.0 98.8 NP_286008 (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86881 87549 + yagY/ecpB 100.0 98.1 NP_286009 (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86236 86823 + yagZ/ecpA 100.0 99.0 NP_286010 (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 85571 86161 + ykgK/ecpR 100.0 97.0 NP_286011 (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
ID089
## Error in read.table("ID089_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00023 35665 37093 + aslA 100.0 92.9 AAG10151 (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005 153477 153932 + csgB 99.8 83.6 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 152072 152722 - csgD 100.0 81.3 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 151237 151653 - csgF 99.0 81.2 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 150377 151210 - csgG 100.0 83.5 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012 99370 100116 - entA 100.0 95.7 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00099 257 1003 + entA 100.0 98.4 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100116 100973 - entB 100.0 98.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 102607 103794 - entC 100.0 97.9 NP_752611 (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 105 875 - entD 100.0 95.2 NP_752599 (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100987 102597 - entE 100.0 95.4 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 4803 8656 + entF 99.3 95.6 NP_752604 (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 105117 106367 - entS 100.0 95.4 NP_752609 (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003 88782 90681 - espL1 100.0 97.6 NP_288154 (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 88201 90387 + espL4 100.0 97.3 NP_290644 (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015 12139 13193 - espR1 83.7 94.1 NP_287686 (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 102593 104013 + espX1 99.9 95.3 NP_285716 (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 58405 59985 - espX4 100.0 96.5 NP_290672 (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 27599 28891 + espX5 100.0 97.0 NP_290699 (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 63516 64327 - espY1 99.9 87.0 NP_285753 (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006 78302 82550 - fdeC 99.9 94.2 YP_002390132 (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00066 900 3140 - fepA 100.0 96.7 NP_752600 (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 104157 105113 + fepB 100.0 97.5 NP_752610 (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 108468 109283 + fepC 100.0 97.3 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 106466 107482 + fepD 100.0 96.1 NP_752608 (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 107479 108471 + fepG 100.0 94.1 NP_752607 (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 3383 4585 + fes 100.0 96.7 NP_752602 (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00050 21169 23555 - fimD 90.5 98.7 NP_757244 (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20629 21162 - fimF 100.0 97.9 NP_757245 (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20113 20616 - fimG 100.0 97.8 NP_757247 (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 19191 20102 - fimH 100.0 97.5 NP_757248 (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035 903 2753 + gspD 100.0 97.0 YP_404600 (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 2753 4246 + gspE 100.0 96.5 YP_404601 (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 4246 5445 + gspF 100.0 96.0 YP_404602 (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5486 5941 + gspG 100.0 95.0 YP_404603 (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5978 6508 + gspH 100.0 95.3 YP_404604 (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6505 6876 + gspI 100.0 95.2 YP_404605 (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6909 7478 + gspJ 100.0 96.7 YP_404606 (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 7475 8452 + gspK 100.0 96.7 YP_404607 (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 8767 9627 + gspL 100.0 97.1 YP_404608 (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 9743 10165 + gspM 100.0 97.9 YP_404609 (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005 69490 70530 - ompA 100.0 98.1 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006 91657 92410 + yagV/ecpE 99.7 97.1 NP_286006 (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 90090 91733 + yagW/ecpD 100.0 99.1 NP_286007 (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 87575 90100 + yagX/ecpC 100.0 98.8 NP_286008 (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86881 87549 + yagY/ecpB 100.0 98.1 NP_286009 (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86236 86823 + yagZ/ecpA 100.0 99.0 NP_286010 (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 85571 86161 + ykgK/ecpR 100.0 97.0 NP_286011 (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
ID186
## Error in read.table("ID186_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00023 35665 37093 + aslA 100.0 92.9 AAG10151 (aslA) putative arylsulfatase [AslA (VF0238)] [Escherichia coli O18:K1:H7 str. RS218]
contig00005 153477 153932 + csgB 99.8 83.6 NP_460114 (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 152072 152722 - csgD 100.0 81.3 NP_460113 (csgD) DNA-binding transcriptional regulator CsgD [curli fibers/thin aggregative fimbriae (AGF) (AI094)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 151237 151653 - csgF 99.0 81.2 NP_460111 (csgF) curli production assembly/transport protein CsgF [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00005 150377 151210 - csgG 100.0 83.5 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00012 99370 100116 - entA 100.0 95.7 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00099 257 1003 + entA 100.0 98.4 NP_752614 (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100116 100973 - entB 100.0 98.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 102607 103794 - entC 100.0 97.9 NP_752611 (entC) isochorismate synthase 1 [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 105 875 - entD 100.0 95.2 NP_752599 (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 100987 102597 - entE 100.0 95.4 NP_752612 (entE) 23-dihydroxybenzoate-AMP ligase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 4803 8656 + entF 99.3 95.6 NP_752604 (entF) enterobactin synthase multienzyme complex component ATP-dependent [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 105117 106367 - entS 100.0 95.4 NP_752609 (entS) enterobactin exporter iron-regulated [enterobactin (IA019)] [Escherichia coli CFT073]
contig00003 88782 90681 - espL1 100.0 97.6 NP_288154 (espL1) Type III secretion system effector espL1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 88201 90387 + espL4 100.0 97.3 NP_290644 (espL4) Type III secretion system effector EspL4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00015 12139 13193 - espR1 83.7 94.1 NP_287686 (espR1) Type III secretion system effector espR1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 102593 104013 + espX1 99.9 95.3 NP_285716 (espX1) Type III secretion system effector EspX1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 58405 59985 - espX4 100.0 96.5 NP_290672 (espX4) Type III secretion system effector EspX4 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00016 27599 28891 + espX5 100.0 97.0 NP_290699 (espX5) Type III secretion system effector EspX5 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00013 63516 64327 - espY1 99.9 87.0 NP_285753 (espY1) Type III secretion system effector EspY1 [LEE encoded T3SS (SS020)] [Escherichia coli O157:H7 str. EDL933]
contig00006 78302 82550 - fdeC 99.9 94.2 YP_002390132 (fdeC) adhesin FdeC [FdeC (VF0506)] [Escherichia coli O45:K1:H7 str. S88]
contig00066 900 3140 - fepA 100.0 96.7 NP_752600 (fepA) ferrienterobactin outer membrane transporter [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 104157 105113 + fepB 100.0 97.5 NP_752610 (fepB) ferrienterobactin ABC transporter periplasmic binding protein [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 108468 109283 + fepC 100.0 97.3 NP_752606 (fepC) ferrienterobactin ABC transporter ATPase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 106466 107482 + fepD 100.0 96.1 NP_752608 (fepD) ferrienterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00012 107479 108471 + fepG 100.0 94.1 NP_752607 (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00066 3383 4585 + fes 100.0 96.7 NP_752602 (fes) enterobactin/ferric enterobactin esterase [enterobactin (IA019)] [Escherichia coli CFT073]
contig00050 21169 23555 - fimD 90.5 98.7 NP_757244 (fimD) Outer membrane usher protein fimD precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20629 21162 - fimF 100.0 97.9 NP_757245 (fimF) FimF protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 20113 20616 - fimG 100.0 97.8 NP_757247 (fimG) FimG protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00050 19191 20102 - fimH 100.0 97.5 NP_757248 (fimH) FimH protein precursor [Type 1 fimbriae (VF0221)] [Escherichia coli CFT073]
contig00035 903 2753 + gspD 100.0 97.0 YP_404600 (gspD) general secretion pathway protein D [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 2753 4246 + gspE 100.0 96.5 YP_404601 (gspE) general secretion pathway protein E [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 4246 5445 + gspF 100.0 96.0 YP_404602 (gspF) general secretion pathway protein F [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5486 5941 + gspG 100.0 95.0 YP_404603 (gspG) general secretion pathway protein G [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 5978 6508 + gspH 100.0 95.3 YP_404604 (gspH) general secretion pathway protein H [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6505 6876 + gspI 100.0 95.2 YP_404605 (gspI) general secretion pathway protein I [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 6909 7478 + gspJ 100.0 96.7 YP_404606 (gspJ) general secretion pathway protein J [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 7475 8452 + gspK 100.0 96.7 YP_404607 (gspK) general secretion pathway protein K [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 8767 9627 + gspL 100.0 97.1 YP_404608 (gspL) general secretion pathway protein L [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00035 9743 10165 + gspM 100.0 97.9 YP_404609 (gspM) general secretion pathway protein M [T2SS (VF0333)] [Shigella dysenteriae Sd197]
contig00005 69490 70530 - ompA 100.0 98.1 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
contig00006 91657 92410 + yagV/ecpE 99.7 97.1 NP_286006 (yagV/ecpE) E. coli common pilus chaperone EcpE [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 90090 91733 + yagW/ecpD 100.0 99.1 NP_286007 (yagW/ecpD) polymerized tip adhesin of ECP fibers [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 87575 90100 + yagX/ecpC 100.0 98.8 NP_286008 (yagX/ecpC) E. coli common pilus usher EcpC [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86881 87549 + yagY/ecpB 100.0 98.1 NP_286009 (yagY/ecpB) E. coli common pilus chaperone EcpB [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 86236 86823 + yagZ/ecpA 100.0 99.0 NP_286010 (yagZ/ecpA) E. coli common pilus structural subunit EcpA [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
contig00006 85571 86161 + ykgK/ecpR 100.0 97.0 NP_286011 (ykgK/ecpR) regulator protein EcpR [ECP (VF0404)] [Escherichia coli O157:H7 str. EDL933]
ID259
Contig Start End Strand Gene Coverage Identity Accession Product
contig00033 15912 16745 + csgG 100.0 80.6 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00228 594 1444 + entB 99.1 80.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021 40218 41263 + ompA 99.0 84.5 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO015E
## Error in read.table("ORTHO015E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00033 15912 16745 + csgG 100.0 80.6 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00228 594 1444 + entB 99.1 80.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021 40218 41263 + ompA 99.0 84.5 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO037E
## Error in read.table("ORTHO037E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00033 15912 16745 + csgG 100.0 80.6 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00228 594 1444 + entB 99.1 80.0 NP_752613 (entB) isochorismatase [Enterobactin (VF0228)] [Escherichia coli CFT073]
contig00021 40218 41263 + ompA 99.0 84.5 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO047E
Contig Start End Strand Gene Coverage Identity Accession Product
contig00107 469 583 + astA 98.3 91.3 BAA94855 (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00161 6225 7058 - csgG 100.0 80.3 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00048 17902 18947 + ompA 99.0 84.9 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO05E
## Error in read.table("ORTHO05E_vfdb.tab", header = T, sep = "\t", dec = ".", : no lines available in input
Contig Start End Strand Gene Coverage Identity Accession Product
contig00107 469 583 + astA 98.3 91.3 BAA94855 (astA) heat-stable enterotoxin 1 [EAST1 (VF0216)] [Escherichia coli O44:H18 042]
contig00161 6225 7058 - csgG 100.0 80.3 NP_460110 (csgG) curli production assembly/transport protein CsgG [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
contig00048 17902 18947 + ompA 99.0 84.9 AAF37887 (ompA) outer membrane protein A [OmpA (VF0236)] [Escherichia coli O18:K1:H7 str. RS218]
ORTHO082EII
Contig Start End Strand Gene Coverage Identity Accession Product
contig00151 8790 10222 + alg8 96.5 82.7 NP_252231 (alg8) alginate-c5-mannuronan-epimerase AlgG [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1]
contig00135 3031 4437 - algA 97.2 81.9 NP_252241 (algA) phosphomannose isomerase / guanosine 5’-diphospho-D-mannose pyrophosphorylase [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1]
contig00135 6486 7769 - algI 82.1 86.2 NP_252238 (algI) alginate o-acetyltransferase AlgI [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1]
contig00027 5006 5587 + algU 100.0 82.5 NP_249453 (algU) alginate biosynthesis protein AlgZ/FimS [Alginate (VF0091)] [Pseudomonas aeruginosa PAO1]
contig00934 767 1574 - fleN 95.7 83.2 NP_250145 (fleN) flagellar synthesis regulator FleN [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00061 4146 5621 - fleQ 99.7 80.0 NP_249788 (fleQ) transcriptional regulator FleQ [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00198 2371 2814 - flgC 100.0 80.9 NP_249769 (flgC) flagellar basal-body rod protein FlgC [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00562 975 1744 + flgG 97.7 86.1 NP_249773 (flgG) flagellar basal-body rod protein FlgG [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00562 1841 2491 + flgH 93.2 81.5 NP_249774 (flgH) flagellar L-ring protein precursor FlgH [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00562 2561 3613 + flgI 94.9 85.7 NP_249775 (flgI) flagellar P-ring protein precursor FlgI [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00381 280 2396 - flhA 99.3 81.6 NP_250143 (flhA) flagellar biosynthesis protein FlhA [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00934 13 723 - fliA 95.0 80.3 NP_250146 (fliA) flagellar biosynthesis sigma factor FliA [Deoxyhexose linking sugar 209 Da capping structure (AI138)] [Pseudomonas aeruginosa PAO1]
contig00844 665 1682 + fliG 99.8 84.7 NP_249793 (fliG) flagellar motor switch protein G [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig01095 511 1479 - fliM 99.6 85.9 NP_250134 (fliM) flagellar motor switch protein FliM [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig00381 4747 5464 - fliP 93.1 83.1 NP_250137 (fliP) flagellar biosynthetic protein FliP [Flagella (VF0273)] [Pseudomonas aeruginosa PAO1]
contig02313 684 885 + mbtH-like 92.2 88.6 NP_251102 (mbtH-like) MbtH-like protein from the pyoverdine cluster [pyoverdine (IA001)] [Pseudomonas aeruginosa PAO1]
contig00682 2148 2884 - motC 99.3 82.0 NP_250151 (motC) flagellar motor protein [Deoxyhexose linking sugar 209 Da capping structure (AI138)] [Pseudomonas aeruginosa PAO1]
contig00319 5118 5450 - pilH 91.0 80.2 NP_249100 (pilH) twitching motility protein PilH [Type IV pili (VF0082)] [Pseudomonas aeruginosa PAO1]
contig00661 555 1873 + pvdH 93.5 80.8 NP_251103 (pvdH) diaminobutyrate-2-oxoglutarate aminotransferase PvdH [pyoverdine (IA001)] [Pseudomonas aeruginosa PAO1]
contig00109 469 978 + pvdS 90.4 82.3 NP_251116 (pvdS) extracytoplasmic-function sigma-70 factor [Pyoverdine (VF0094)] [Pseudomonas aeruginosa PAO1]
contig00146 2638 3618 + waaF 94.5 81.5 NP_253699 (waaF) heptosyltransferase I [LPS (VF0085)] [Pseudomonas aeruginosa PAO1]


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Multi-Locus Sequence Typing (MLST)


Symbol Meaning
~ novel full length allele similar to match
? partial match to known allele
- allele missing


Scheme ST 1 2 3 4 5 6 7
ID003II - -
ID012II abaumannii_2 1 Pas_cpn60(1) Pas_fusA(1) Pas_gltA(1) Pas_pyrG(1) Pas_recA(5) Pas_rplB(1) Pas_rpoB(1)
ID014II ecoli 167 adk(10) fumC(11) gyrB(4) icd(8) mdh(8) purA(13) recA(2)
ID030 - -
ID063 ecoli 48 adk(6) fumC(11) gyrB(4) icd(8) mdh(8) purA(8) recA(2)
ID089 abaumannii_2 - Pas_cpn60(~199) Pas_fusA(~186) Pas_gltA(185) Pas_pyrG(91) Pas_recA(~194) Pas_rplB(101) Pas_rpoB(169)
ID186 abaumannii_2 1 Pas_cpn60(1) Pas_fusA(1) Pas_gltA(1) Pas_pyrG(1) Pas_recA(5) Pas_rplB(1) Pas_rpoB(1)
ID259 ecloacae 414 dnaA(136) fusA(99) gyrB(153) leuS(160) pyrG(140) rplB(12) rpoB(92)
ORTHO015E abaumannii_2 52 Pas_cpn60(3) Pas_fusA(2) Pas_gltA(2) Pas_pyrG(7) Pas_recA(9) Pas_rplB(1) Pas_rpoB(5)
ORTHO037E abaumannii_2 1 Pas_cpn60(1) Pas_fusA(1) Pas_gltA(1) Pas_pyrG(1) Pas_recA(5) Pas_rplB(1) Pas_rpoB(1)
ORTHO047E ecloacae 515 dnaA(56) fusA(38) gyrB(35) leuS(58) pyrG(169) rplB(12) rpoB(20)
ORTHO05E - -
ORTHO082EII pputida 12 argS(8) gyrB(11) ileS(52) nuoC(31) ppsA(51) recA(55) rpoB(20)
rpoD(52)

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Pangenome Analysis

Pangenome genes summary

Genes Description Number
Core genes (99% <= strains <= 100%) 0
Soft core genes (95% <= strains < 99%) 0
Shell genes (15% <= strains < 95%) 18812
Cloud genes (0% <= strains < 15%) 22545
Total genes (0% <= strains <= 100%) 41357

Schematic representation of genes presence (color) or absence (blank) between samples:


Pangenome tree based on presence/absence of accessory genes representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Pangenome tree based on core genome alignment representation

Rectangular (phylogram)

Circular (phylogram)

Circular (cladogram)


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Insertion sequence characterization


Field Description
Region Numeric code given to insertion sequence (IS)
Orientation The orientation of IS position: Either forward (F) or reverse (F)
X-cordinates The left coordinate of the position
Y-coordinates The right coordinate of the position
Gap The distance between the x and y coordinates
CallType Describes whether a position hit is novel (not in reference) or known (in the reference)
LeftGene Locus tag ID of the gene closest to the left side of the IS position
LeftGeneDescription Description of the gene feature from the left side of the IS position. By default this is the product position
RightGene Locus tag ID of the gene closest to the right side of the IS position
RightGeneDescription Description of the gene feature from the right side of the IS position. By default this is the product position


Select the sample

ID012II
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 464044 464067 23 novel* IX87_RS02500 biotin synthase BioB IX87_RS02500 biotin synthase BioB
region_2 R 545223 545299 76 novel* IX87_RS02925 taurine ABC transporter substrate-binding protein IX87_RS21895 IS5-like element ISAba27 family transposase
region_3 F 1366525 1366525 0 novel IX87_RS07030 CoA-acylating methylmalonate-semialdehyde dehydrogenase IX87_RS07035 aspartate aminotransferase family protein
region_4 R 1608582 1609776 1194 known IX87_RS08350 GTP cyclohydrolase I FolE IX87_RS08365 ADC family extended-spectrum class C beta-lactamase
region_5 F 3999793 3999801 -8 novel IX87_RS19915 hypothetical protein IX87_RS19915 hypothetical protein
ID186
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 836088 836097 -9 novel IX87_RS04290 minor capsid protein IX87_RS04290 minor capsid protein
region_2 R 1608610 1609783 1173 known IX87_RS08350 GTP cyclohydrolase I FolE IX87_RS08365 ADC family extended-spectrum class C beta-lactamase
region_3 F 1647298 1647377 79 novel* IX87_RS08505 TetR/AcrR family transcriptional regulator IX87_RS08505 TetR/AcrR family transcriptional regulator
ORTHO015E
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 FALSE 1524434 1524445 11 novel IX87_RS07860 EAL domain-containing protein IX87_RS07860 EAL domain-containing protein
region_1 FALSE 1611087 1611097 -10 novel IX87_RS08370 DUF4105 domain-containing protein IX87_RS08370 DUF4105 domain-containing protein
ORTHO037E
Region Orientation X-coordinates Y-coordinates Gap CallType LeftGene LeftGeneDescription RightGene RightGeneDescription
region_1 F 836082 836088 6 novel IX87_RS04290 minor capsid protein IX87_RS04290 minor capsid protein
region_2 R 1608602 1609765 1163 known IX87_RS08350 GTP cyclohydrolase I FolE IX87_RS08365 ADC family extended-spectrum class C beta-lactamase
region_3 R 3393469 3394675 1206 known IX87_RS16895 EAL domain-containing protein IX87_RS16910 TetR/AcrR family transcriptional regulator


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Citations and Bibliography

If you have used rMAP, please cite:

Sserwadda, I., & Mboowa, G. (2021). rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data. Microbial genomics, 7(6), 10.1099/mgen.0.000583. https://doi.org/10.1099/mgen.0.000583


The philosophy of rMAP was built on the foundation of already pre-existing tools. As a token of gratitude to the authors of those numerous tools, please also cite:


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